Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance

Natural Organic Matter Enhances Natural Transformation of Extracellular Antibiotic Resistance Genes in Sunlit Water

Antibiotic resistance genes (ARGs) as emerging environmental contaminants exacerbate the risk of spreading antibiotic resistance. Natural organic matter (NOM) is ubiquitous in aquatic environments and plays a crucial role in biogeochemical cycles. However, its impact on the dissemination of extracellular antibiotic resistance genes (eARGs) under sunlight exposure remains elusive. This study reveals that environmentally relevant levels of NOM (0.1-20 mg/L) can significantly enhance the natural transformation frequency of the model bacterium Acinetobacter baylyi ADP1 by up to 7.6-fold under simulated sunlight. Similarly, this enhancement was consistently observed in natural water and wastewater systems. Further mechanism analysis revealed that reactive oxygen species (ROS) generated by NOM under sunlight irradiation, primarily singlet oxygen and hydroxyl radicals, play a crucial role in this process. These ROS induce intracellular oxidative stress and elevated cellular membrane permeability, thereby indirectly boosting ATP production and enhancing cell competence of extracellular DNA uptake and integration. Our findings highlight a previously underestimated role of natural factors in the dissemination of eARGs within aquatic ecosystems and deepen our understanding of the complex interplay between NOM, sunlight, and microbes in environmental water bodies. This underscores the importance of developing comprehensive strategies to mitigate the spread of antibiotic resistance in aquatic environments.

Engineering Microbial Consortia as Living Materials: Advances and Prospectives

The field of Engineered Living Materials (ELMs) integrates engineered living organisms into natural biomaterials to achieve diverse objectives. Multiorganism consortia, prevalent in both naturally occurring and synthetic microbial cultures, exhibit complex functionalities and interrelationships, extending the scope of what can be achieved with individual engineered bacterial strains. However, the ELMs comprising microbial consortia are still in the developmental stage. In this Review, we introduce two strategies for designing ELMs constituted of microbial consortia: a top-down strategy, which involves characterizing microbial interactions and mimicking and reconstructing natural ecosystems, and a bottom-up strategy, which entails the rational design of synthetic consortia and their assembly with material substrates to achieve user-defined functions. Next, we summarize technologies from synthetic biology that facilitate the efficient engineering of microbial consortia for performing tasks more complex than those that can be done with single bacterial strains. Finally, we discuss essential challenges and future perspectives for microbial consortia-based ELMs.

Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment

The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.

Quantification of β-lactamase producing bacteria in German surface waters with subsequent MALDI-TOF MS-based identification and β-lactamase activity assay

Environmental oligotrophic bacteria are suspected to be highly relevant carriers of antimicrobial resistance (AMR). However, there is a lack of validated methods for monitoring in the aquatic environment. Since extended-spectrum β-lactamases (ESBLs) play a particularly important role in the clinical sector, a culturing method based on R2A-medium spiked with different combinations of β-lactams was applied to quantify β-lactamase-producing environmental bacteria from surface waters. In German surface water samples (n = 28), oligotrophic bacteria ranging from 4.0 × 103 to 1.7 × 104 CFU per 100 mL were detected on the nutrient-poor medium spiked with 3rd generation cephalosporins and carbapenems. These numbers were 3 log10 higher compared to ESBL-producing Enterobacteriales of clinical relevance from the same water samples. A MALDI-TOF MS identification of the isolates demonstrated, that the method leads to the isolation of environmentally relevant strains with Pseudomonas, Flavobacterium, and Janthinobacterium being predominant β-lactam resistant genera. Subsequent micro-dilution antibiotic susceptibility tests (Micronaut-S test) confirmed the expression of β-lactamases. The qPCR analysis of surface waters DNA extracts showed the presence of β-lactamase genes (blaTEM, blaCMY-2, blaOXA-48, blaVIM-2, blaSHV, and blaNDM-1) at concentrations of 3.7 (±1.2) to 1.0 (±1.9) log10 gene copies per 100 mL. Overall, the results demonstrate a widespread distribution of cephalosporinase and carbapenemase enzymes in oligotrophic environmental bacteria that have to be considered as a reservoir of ARGs and contribute to the spread of antibiotic resistance.

Microfluidic approaches in microbial ecology

Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.

The priority of yeast to select among various DNA options to repair genome breaks by homologous recombination

BACKGROUND

Horizontal gene transfer (HGT) is considered an important mechanism to contribute to the evolution of bacteria, plants, and animals by allowing the movement of genetic material between organisms, in difference to vertical inheritance. Thereby it can also play a significant role in spreading traits like antibiotic resistance among bacteria and virulence factors between pathogens. During the HGT, organisms take up free DNA from the environment and incorporate it into their genomes. Although HGT is known to be carried out by many organisms, there is limited information on how organisms select which genetic material for horizontal transfer. Here we have investigated the preference priority of Saccharomyces cerevisiae between different options of gene source presented under certain stress conditions to repair a double-strand break (DSB) in DNA via HR.

RESULTS

Each genetic module was designed with appropriate sequences being homologous for two sides of the DSB, which is important for yeast to repair the fracture with HR. S. cerevisiae made a random selection between two heterologous T1 (44%) and T2 (56%) modules to repair DSB. Interestingly, yeast corrected the DNA break only with the T3 module (almost 100%) when the homologous T3 module was an option for the selection. It seems that S. cerevisiae tends to prefer T3 over alternatives to fix DSBs when it exists among the options.

CONCLUSIONS

It seems that S. cerevisiae have a preference for priority to select a particular one under certain conditions when it has various DNA options to repair a DSB in its genome, further studies are required to support our findings.

Proton pump inhibitors increase the risk of carbapenem-resistant Enterobacteriaceae colonization by facilitating the transfer of antibiotic resistance genes among bacteria in the gut microbiome

Carbapenem-resistant Enterobacteriaceae (CRE) pose a global health threat; however, there is still limited understanding of the risk factors and underlying mechanisms of CRE colonization in the gut microbiome. We conducted a matched case-control study involving 282 intensive care unit patients to analyze influencing covariates on CRE colonization. Subsequently, their effects on the gut microbiome were analyzed in a subset of 98 patients (47 CRE carriers and 51 non-CRE carriers) using whole metagenome sequences. The concomitant use of proton pump inhibitors (PPIs) and antibiotics was a significant risk factor for CRE colonization. The gut microbiome differed according to PPI administration, even within the CRE and non-CRE groups. Moreover, the transfer of mobile genetic elements (MGEs) harboring carbapenem resistance genes (CRGs) between bacteria was higher in the PPI-treated group than in the PPI-not-treated group among CRE carriers. The concomitant use of PPIs and antibiotics significantly alters the gut microbiome and increases the risk of CRE colonization by facilitating the transfer of CRGs among bacteria of the gut microbiome. Based on these findings, improved stewardship of PPIs as well as antibiotics can provide strategies to reduce the risk of CRE colonization, thereby potentially improving patient prognosis.

Comparative resistome analysis of Aeromonas species in aquaculture reveals antibiotic resistance patterns and phylogeographic distribution

The overuse of antibiotics in aquaculture drives the emergence of multi-drug-resistant bacteria, and antibiotic-resistant genes (ARGs) can be disseminated to other bacteria through vertical- and horizontal gene transfer (VGT and HGT) under selective pressure. Profiling the antibiotic resistome and understanding the global distribution of ARGs constitutes the first step in developing a control strategy. Hence, this study utilized extensive genomic data from hundreds of Aeromonas strains in aquaculture to profile resistome patterns and explores their association with isolation year, country, and species characteristics. Overall, ∼400 Aeromonas genomes were used to predict the ARGs from A. salmonicida, A. hydrophila, A. veronii, A. media, and A. sobria. ARGs such as sul1, tet(A), and tet(D), which display a similar proportion of positive strains among species, were subjected to phylodynamic and phylogeographic analyses. More than a hundred ARGs were identified, some of which exhibited either species-specific or non-species-specific patterns. A. salmonicida and A. media were found to have a higher proportion of species-specific ARGs than other strains, which might lead to more distinct patterns of ARG acquisition. Overall, ∼25% of strains have either sul1, tet(A), or tet(D) gene(s), but no significant difference was observed in the proportion of positive strains by species. Phylogeographic analysis revealed that the abundant numbers of sul1, tet(A), and/or tet(D) introduced in a few East Asian and North American countries could spread to both adjacent and faraway countries. In recent years, the proportions of these ARGs have dramatically increased, particularly in strains sourced from aquatic environments, suggesting control is required of the overuse of antibiotics in aquaculture. The findings of this research offer significant insights into the global dissemination of ARGs.

Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics

The ability to effectively represent microbiome dynamics is a crucial challenge in their quantitative analysis and engineering. By using autoencoder neural networks, we show that microbial growth dynamics can be compressed into low-dimensional representations and reconstructed with high fidelity. These low-dimensional embeddings are just as effective, if not better, than raw data for tasks such as identifying bacterial strains, predicting traits like antibiotic resistance, and predicting community dynamics. Additionally, we demonstrate that essential dynamical information of these systems can be captured using far fewer variables than traditional mechanistic models. Our work suggests that machine learning can enable the creation of concise representations of high-dimensional microbiome dynamics to facilitate data analysis and gain new biological insights.

Interfacial morphodynamics of proliferating microbial communities

In microbial communities, various cell types often coexist by occupying distinct spatial domains. What determines the shape of the interface between such domains-which in turn influences the interactions between cells and overall community function? Here, we address this question by developing a continuum model of a 2D spatially-structured microbial community with two distinct cell types. We find that, depending on the balance of the different cell proliferation rates and substrate friction coefficients, the interface between domains is either stable and smooth, or unstable and develops finger-like protrusions. We establish quantitative principles describing when these different interfacial behaviors arise, and find good agreement both with the results of previous experimental reports as well as new experiments performed here. Our work thus helps to provide a biophysical basis for understanding the interfacial morphodynamics of proliferating microbial communities, as well as a broader range of proliferating active systems.

Acinetobacter type VI secretion system comprises a non-canonical membrane complex

A. baumannii can rapidly acquire new resistance mechanisms and persist on abiotic surface, enabling the colonization of asymptomatic human host. In Acinetobacter the type VI secretion system (T6SS) is involved in twitching, surface motility and is used for interbacterial competition allowing the bacteria to uptake DNA. A. baumannii possesses a T6SS that has been well studied for its regulation and specific activity, but little is known concerning its assembly and architecture. The T6SS nanomachine is built from three architectural sub-complexes. Unlike the baseplate (BP) and the tail-tube complex (TTC), which are inherited from bacteriophages, the membrane complex (MC) originates from bacteria. The MC is the most external part of the T6SS and, as such, is subjected to evolution and adaptation. One unanswered question on the MC is how such a gigantesque molecular edifice is inserted and crosses the bacterial cell envelope. The A. baumannii MC lacks an essential component, the TssJ lipoprotein, which anchors the MC to the outer membrane. In this work, we studied how A. baumannii compensates the absence of a TssJ. We have characterized for the first time the A. baumannii's specific T6SS MC, its unique characteristic, its membrane localization, and assembly dynamics. We also defined its composition, demonstrating that its biogenesis employs three Acinetobacter-specific envelope-associated proteins that define an intricate network leading to the assembly of a five-proteins membrane super-complex. Our data suggest that A. baumannii has divided the function of TssJ by (1) co-opting a new protein TsmK that stabilizes the MC and by (2) evolving a new domain in TssM for homo-oligomerization, a prerequisite to build the T6SS channel. We believe that the atypical species-specific features we report in this study will have profound implication in our understanding of the assembly and evolutionary diversity of different T6SSs, that warrants future investigation.

Engineered bacteria detect tumor DNA

Synthetic biology has developed sophisticated cellular biosensors to detect and respond to human disease. However, biosensors have not yet been engineered to detect specific extracellular DNA sequences and mutations. Here, we engineered naturally competent Acinetobacter baylyi to detect donor DNA from the genomes of colorectal cancer (CRC) cells, organoids, and tumors. We characterized the functionality of the biosensors in vitro with coculture assays and then validated them in vivo with sensor bacteria delivered to mice harboring colorectal tumors. We observed horizontal gene transfer from the tumor to the sensor bacteria in our mouse model of CRC. This cellular assay for targeted, CRISPR-discriminated horizontal gene transfer (CATCH) enables the biodetection of specific cell-free DNA.

Testing for the fitness benefits of natural transformation during community-embedded evolution

Natural transformation is a process where bacteria actively take up DNA from the environment and recombine it into their genome or reconvert it into extra-chromosomal genetic elements. The evolutionary benefits of transformation are still under debate. One main explanation is that foreign allele and gene uptake facilitates natural selection by increasing genetic variation, analogous to meiotic sex. However, previous experimental evolution studies comparing fitness gains of evolved transforming- and isogenic non-transforming strains have yielded mixed support for the 'sex hypothesis.' Previous studies testing the sex hypothesis for natural transformation have largely ignored species interactions, which theory predicts provide conditions favourable to sex. To test for the adaptive benefits of bacterial transformation, the naturally transformable wild-type Acinetobacter baylyi and a transformation-deficient ∆comA mutant were evolved for 5 weeks. To provide strong and potentially fluctuating selection, A. baylyi was embedded in a community of five other bacterial species. DNA from a pool of different Acinetobacter strains was provided as a substrate for transformation. No effect of transformation ability on the fitness of evolved populations was found, with fitness increasing non-significantly in most treatments. Populations showed fitness improvement in their respective environments, with no apparent costs of adaptation to competing species. Despite the absence of fitness effects of transformation, wild-type populations evolved variable transformation frequencies that were slightly greater than their ancestor which potentially could be caused by genetic drift.

Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK

Non-typhoidal Salmonella (NTS) is a major cause of bacterial gastroenteritis. Although many countries have implemented whole genome sequencing (WGS) of NTS, there is limited knowledge on NTS diversity on food and its contribution to human disease. In this study, the aim was to characterise the NTS genomes from retail foods in a particular region of the UK and assess the contribution to human NTS infections. Raw food samples were collected at retail in a repeated cross-sectional design in Norfolk, UK, including chicken (n=311), leafy green (n=311), pork (n=311), prawn (n=279) and salmon (n=157) samples. Up to eight presumptive NTS isolates per positive sample underwent WGS and were compared to publicly available NTS genomes from UK human cases. NTS was isolated from chicken (9.6 %), prawn (2.9 %) and pork (1.3 %) samples and included 14 serovars, of which Salmonella Infantis and Salmonella Enteritidis were the most common. The S. Enteritidis isolates were only isolated from imported chicken. No antimicrobial resistance determinants were found in prawn isolates, whilst 5.1 % of chicken and 0.64 % of pork samples contained multi-drug resistant NTS. The maximum number of pairwise core non-recombinant single nucleotide polymorphisms (SNPs) amongst isolates from the same sample was used to measure diversity and most samples had a median of two SNPs (range: 0-251). NTS isolates that were within five SNPs to clinical UK isolates belonged to specific serovars: S. Enteritidis and S. Infantis (chicken), and S. I 4,[5],12:i- (pork and chicken). Most NTS isolates that were closely related to human-derived isolates were obtained from imported chicken, but further epidemiological data are required to assess definitively the probable source of the human cases. Continued WGS surveillance of Salmonella on retail food involving multiple isolates from each sample is necessary to capture the diversity of Salmonella and determine the relative importance of different sources of human disease.

Large-scale analysis of putative plasmids in clinical multidrug-resistant Escherichia coli isolates from Vietnamese patients

Introduction

In the past decades, extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Escherichia coli isolates have been detected in Vietnamese hospitals. The transfer of antimicrobial resistance (AMR) genes carried on plasmids is mainly responsible for the emergence of multidrug-resistant E. coli strains and the spread of AMR genes through horizontal gene transfer. Therefore, it is important to thoroughly study the characteristics of AMR gene-harboring plasmids in clinical multidrug-resistant bacterial isolates.

Methods

The profiles of plasmid assemblies were determined by analyzing previously published whole-genome sequencing data of 751 multidrug-resistant E. coli isolates from Vietnamese hospitals in order to identify the risk of AMR gene horizontal transfer and dissemination.

Results

The number of putative plasmids in isolates was independent of the sequencing coverage. These putative plasmids originated from various bacterial species, but mostly from the Escherichia genus, particularly E. coli species. Many different AMR genes were detected in plasmid contigs of the studied isolates, and their number was higher in CR isolates than in ESBL-producing isolates. Similarly, the bla_KPC-2, bla_NDM-5, bla_OXA-1, bla_OXA-48, and bla_OXA-181 β-lactamase genes, associated with resistance to carbapenems, were more frequent in CR strains. Sequence similarity network and genome annotation analyses revealed high conservation of the β-lactamase gene clusters in plasmid contigs that carried the same AMR genes.

Discussion

Our study provides evidence of horizontal gene transfer in multidrug-resistant E. coli isolates via conjugative plasmids, thus rapidly accelerating the emergence of resistant bacteria. Besides reducing antibiotic misuse, prevention of plasmid transmission also is essential to limit antibiotic resistance.

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing

The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L^-1). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L^-1). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.

Predicting partner fitness based on spatial structuring in a light-driven microbial community

Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology (e.g., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.

Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia

Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.

Efficient plasmid transfer via natural competence in a microbial co-culture

The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.

Intercepting biological messages: Antibacterial molecules targeting nucleic acids during interbacterial conflicts

Bacteria live in polymicrobial communities and constantly compete for resources. These organisms have evolved an array of antibacterial weapons to inhibit the growth or kill competitors. The arsenal comprises antibiotics, bacteriocins, and contact-dependent effectors that are either secreted in the medium or directly translocated into target cells. During bacterial antagonistic encounters, several cellular components important for life become a weak spot prone to an attack. Nucleic acids and the machinery responsible for their synthesis are well conserved across the tree of life. These molecules are part of the information flow in the central dogma of molecular biology and mediate long- and short-term storage for genetic information. The aim of this review is to summarize the diversity of antibacterial molecules that target nucleic acids during antagonistic interbacterial encounters and discuss their potential to promote the emergence antibiotic resistance.

Type VI Secretion Systems: Environmental and Intra-host Competition of Vibrio cholerae

The Vibrio Type VI Secretion System (T6SS) is a harpoon-like nanomachine that serves as a defense system and is encoded by approximately 25% of all gram-negative bacteria. In this chapter, we describe the structure of the T6SS in different Vibrio species and outline how the use of different T6SS effector and immunity proteins control kin selection. We summarize the genetic loci that encode the structural elements that make up the Vibrio T6SSs and how these gene clusters are regulated. Finally, we provide insights into T6SS-based competitive dynamics, the role of T6SS genetic exchange in those competitive dynamics, and roles for the Vibrio T6SS in virulence.

Antimicrobial and the Resistances in the Environment: Ecological and Health Risks, Influencing Factors, and Mitigation Strategies

Antimicrobial contamination and antimicrobial resistance have become global environmental and health problems. A large number of antimicrobials are used in medical and animal husbandry, leading to the continuous release of residual antimicrobials into the environment. It not only causes ecological harm, but also promotes the occurrence and spread of antimicrobial resistance. The role of environmental factors in antimicrobial contamination and the spread of antimicrobial resistance is often overlooked. There are a large number of antimicrobial-resistant bacteria and antimicrobial resistance genes in human beings, which increases the likelihood that pathogenic bacteria acquire resistance, and also adds opportunities for human contact with antimicrobial-resistant pathogens. In this paper, we review the fate of antimicrobials and antimicrobial resistance in the environment, including the occurrence, spread, and impact on ecological and human health. More importantly, this review emphasizes a number of environmental factors that can exacerbate antimicrobial contamination and the spread of antimicrobial resistance. In the future, the timely removal of antimicrobials and antimicrobial resistance genes in the environment will be more effective in alleviating antimicrobial contamination and antimicrobial resistance.

Advances in linking single-cell bacterial stress response to population-level survival

Stress response mechanisms can allow bacteria to survive a myriad of challenges, including nutrient changes, antibiotic encounters, and antagonistic interactions with other microbes. Expression of these stress response pathways, in addition to other cell features such as growth rate and metabolic state, can be heterogeneous across cells and over time. Collectively, these single-cell-level phenotypes contribute to an overall population-level response to stress. These include diversifying actions, which can be used to enable bet-hedging, and coordinated actions, such as biofilm production, horizontal gene transfer, and cross-feeding. Here, we highlight recent results and emerging technologies focused on both single-cell and population-level responses to stressors, and we draw connections about the combined impact of these effects on survival of bacterial communities.

Ecology and Evolutionary Biology of Hindering Phage Therapy: The Phage Tolerance vs. Phage Resistance of Bacterial Biofilms

As with antibiotics, we can differentiate various acquired mechanisms of bacteria-mediated inhibition of the action of bacterial viruses (phages or bacteriophages) into ones of tolerance vs. resistance. These also, respectively, may be distinguished as physiological insensitivities (or protections) vs. resistance mutations, phenotypic resistance vs. genotypic resistance, temporary vs. more permanent mechanisms, and ecologically vs. also near-term evolutionarily motivated functions. These phenomena can result from multiple distinct molecular mechanisms, many of which for bacterial tolerance of phages are associated with bacterial biofilms (as is also the case for the bacterial tolerance of antibiotics). The resulting inhibitions are relevant from an applied perspective because of their potential to thwart phage-based treatments of bacterial infections, i.e., phage therapies, as well as their potential to interfere more generally with approaches to the phage-based biological control of bacterial biofilms. In other words, given the generally low toxicity of properly chosen therapeutic phages, it is a combination of phage tolerance and phage resistance, as displayed by targeted bacteria, that seems to represent the greatest impediments to phage therapy's success. Here I explore general concepts of bacterial tolerance of vs. bacterial resistance to phages, particularly as they may be considered in association with bacterial biofilms.

Uncovering the Secretion Systems of Acinetobacter baumannii: Structures and Functions in Pathogenicity and Antibiotic Resistance

Infections led by Acinetobacter baumannii strains are of great concern in healthcare environments due to the strong ability of the bacteria to spread through different apparatuses and develop drug resistance. Severe diseases can be caused by A. baumannii in critically ill patients, but its biological process and mechanism are not well understood. Secretion systems have recently been demonstrated to be involved in the pathogenic process, and five types of secretion systems out of the currently known six from Gram-negative bacteria have been found in A. baumannii. They can promote the fitness and pathogenesis of the bacteria by releasing a variety of effectors. Additionally, antibiotic resistance is found to be related to some types of secretion systems. In this review, we describe the genetic and structural compositions of the five secretion systems that exist in Acinetobacter. In addition, the function and molecular mechanism of each secretion system are summarized to explain how they enable these critical pathogens to overcome eukaryotic hosts and prokaryotic competitors to cause diseases.

Calibrating spatiotemporal models of microbial communities to microscopy data: A review

Spatiotemporal models that account for heterogeneity within microbial communities rely on single-cell data for calibration and validation. Such data, commonly collected via microscopy and flow cytometry, have been made more accessible by recent advances in microfluidics platforms and data processing pipelines. However, validating models against such data poses significant challenges. Validation practices vary widely between modelling studies; systematic and rigorous methods have not been widely adopted. Similar challenges are faced by the (macrobial) ecology community, in which systematic calibration approaches are often employed to improve quantitative predictions from computational models. Here, we review single-cell observation techniques that are being applied to study microbial communities and the calibration strategies that are being employed for accompanying spatiotemporal models. To facilitate future calibration efforts, we have compiled a list of summary statistics relevant for quantifying spatiotemporal patterns in microbial communities. Finally, we highlight some recently developed techniques that hold promise for improved model calibration, including algorithmic guidance of summary statistic selection and machine learning approaches for efficient model simulation.

Microfluidics for long-term single-cell time-lapse microscopy: Advances and applications

Cells are inherently dynamic, whether they are responding to environmental conditions or simply at equilibrium, with biomolecules constantly being made and destroyed. Due to their small volumes, the chemical reactions inside cells are stochastic, such that genetically identical cells display heterogeneous behaviors and gene expression profiles. Studying these dynamic processes is challenging, but the development of microfluidic methods enabling the tracking of individual prokaryotic cells with microscopy over long time periods under controlled growth conditions has led to many discoveries. This review focuses on the recent developments of one such microfluidic device nicknamed the mother machine. We overview the original device design, experimental setup, and challenges associated with this platform. We then describe recent methods for analyzing experiments using automated image segmentation and tracking. We further discuss modifications to the experimental setup that allow for time-varying environmental control, replicating batch culture conditions, cell screening based on their dynamic behaviors, and to accommodate a variety of microbial species. Finally, this review highlights the discoveries enabled by this technology in diverse fields, such as cell-size control, genetic mutations, cellular aging, and synthetic biology.

Engineering microbial consortia with rationally designed cellular interactions

Synthetic microbial consortia represent a frontier of synthetic biology that promises versatile engineering of cellular functions. They are primarily developed through the design and construction of cellular interactions that coordinate individual dynamics and generate collective behaviors. Here we review recent advances in the engineering of synthetic communities through cellular-interaction programming. We first examine fundamental building blocks for intercellular communication and unidirectional positive and negative interactions. We then recap the assembly of the building blocks for creating bidirectional interactions in two-species ecosystems, which is followed by the discussion of engineering toward complex communities with increasing species numbers, under spatial contexts, and via model-guided design. We conclude by summarizing major challenges and future opportunities of engineered microbial ecosystems.

High Rates of Multidrug-Resistant Escherichia coli in Great Cormorants (Phalacrocorax carbo) of the German Baltic and North Sea Coasts: Indication of Environmental Contamination and a Potential Public Health Risk

Antimicrobial-resistant bacteria pose a serious global health risk for humans and animals, while the role of wildlife in the dynamic transmission processes of antimicrobial resistance in environmental settings is still unclear. This study determines the occurrence of antimicrobial-resistant Escherichia coli in the free-living great cormorants (Phalacrocorax carbo) of the North and Baltic Sea coasts of Schleswig-Holstein, Germany. For this, resistant E.coli were isolated from cloacal or faecal swabs and their antimicrobial resistance pheno- and genotypes were investigated using disk diffusion tests and PCR assays. The isolates were further assigned to the four major phylogenetic groups, and their affiliation to avian pathogenic E. coli (APEC) was tested. Resistant E. coli were isolated from 66.7% of the 33 samples, and 48.9% of all the resistant isolates showed a multidrug resistance profile. No spatial differences were seen between the different sampling locations with regard to the occurrence of antimicrobial resistance or multidrug resistance. Most commonly, resistance percentages occurred against streptomycin, followed by tetracycline and sulfonamides. More than half of the isolates belonged to the phylogenetic group B1. Of all the isolates, 24.4% were classified as APEC isolates, of which almost 82% were identified as multidrug-resistant. These results add information on the dispersal of antimicrobial-resistant bacteria in wild birds in Germany, thereby allowing conclusions on the degree of environmental contamination and potential public health concerns.

Coexistence of blaNDM-1, blaOXA-51, blaOXA-23 and armA in conjunction with novel mutations detected in RND efflux pump regulators in tigecycline resistant clinical isolates of Acinetobacter baumannii

This study has investigated a total of 51 A. baumannii isolates for the prevalence of resistant determinants in tigecycline susceptible and non-susceptible clinical isolates of A. baumannii. Antimicrobial susceptibility testing revealed 74% of isolates were tigecycline resistant. Mutations in RND-efflux pump regulatory genes and the expression of efflux pump genes were measured in tigecycline resistant isolates. There was a strong co-relation between the blaNDM-1 and armA wherein majority of the isolates that are positive for blaNDM-1 have also harbored armA. Compared with TSAB (tigecycline susceptible A. baumannii), TNAB (tigecycline non-susceptible A. baumannii) isolates show increased distribution of blaNDM-1 (p = 0.048), blaIMP-1 (p<0.0001) and blaOXA-51 (p = 0.0029) carbapenemase genes. The variants of RND-efflux pump regulatory genes due to amino-acid mutations in adeS (F12S, K84E, W61R, N268H and Q299R) and adeL (G21R and Q262R) were identified in tigecycline resistant isolates as well as ISAba1 mediated disruption of adeN were observed causing overexpression of adeIJK efflux pump. Additionally, mutations in adeRS were also associated with increased expression of adeABC efflux pump. Besides, TNAB isolates showed significantly (p<0.0001) higher ability of biofilm formation as compared to TSAB isolates. The tigecycline resistance due to mutations in contemporary A. baumannii isolates having a higher ability to form biofilm may pose therapeutic difficulties.

Effects of hematite on the dissemination of antibiotic resistance in pathogens and underlying mechanisms

The dissemination of antibiotic resistance genes (ARGs) in pathogens is becoming a pervasive global health threat, to which the importance of the environment attracts more and more attention. However, how natural minerals affect ARGs transfer in pathogens is still unclear. In this study, the concentration and size effects of hematite on the ARGs conjugative transfer to a common zoonotic pathogen Escherichia coli O157:H7 and underlying mechanisms were explored. Results revealed that bulk hematite reduced the conjugation of resistant plasmids by inhibiting cell growth at any concentration (1-100 mg/L), different from nano-hematite. Low concentrations of nano-hematite (≤ 25 mg/L) induced significant increases in conjugative transfer frequency of 1.83-4.49 folds, while its high concentrations (50 and 100 mg/L) showed no impact, compared with the control group. This low-concentration effect was likely attributed to the increased intracellular ROS level, the reduced intercellular repulsion by increasing the extracellular polymeric substances production and cell surface hydrophobicity, the formation of transfer channels and the increased membrane permeability evidenced by significant changes in gene expression level, and the increased proton motive force by increasing the transmembrane potential of recipients. These findings shed light on potential health risks caused by nano minerals-mediated ARGs dissemination in pathogens in the environment.

Altered Ecology of the Respiratory Tract Microbiome and Nosocomial Pneumonia

Nosocomial pneumonia is one of the most frequent infections in critical patients. It is primarily associated with mechanical ventilation leading to severe illness, high mortality, and prolonged hospitalization. The risk of mortality has increased over time due to the rise in multidrug-resistant (MDR) bacterial infections, which represent a global public health threat. Respiratory tract microbiome (RTM) research is growing, and recent studies suggest that a healthy RTM positively stimulates the immune system and, like the gut microbiome, can protect against pathogen infection through colonization resistance (CR). Physiological conditions of critical patients and interventions as antibiotics administration and mechanical ventilation dramatically alter the RTM, leading to dysbiosis. The dysbiosis of the RTM of ICU patients favors the colonization by opportunistic and resistant pathogens that can be part of the microbiota or acquired from the hospital environments (biotic or built ones). Despite recent evidence demonstrating the significance of RTM in nosocomial infections, most of the host-RTM interactions remain unknown. In this context, we present our perspective regarding research in RTM altered ecology in the clinical environment, particularly as a risk for acquisition of nosocomial pneumonia. We also reflect on the gaps in the field and suggest future research directions. Moreover, expected microbiome-based interventions together with the tools to study the RTM highlighting the "omics" approaches are discussed.

T6SS secretes an LPS-binding effector to recruit OMVs for exploitative competition and horizontal gene transfer

Outer membrane vesicles (OMVs) can function as nanoscale vectors that mediate bacterial interactions in microbial communities. How bacteria recognize and recruit OMVs inter-specifically remains largely unknown, thus limiting our understanding of the complex physiological and ecological roles of OMVs. Here, we report a ligand-receptor interaction-based OMV recruitment mechanism, consisting of a type VI secretion system (T6SS)-secreted lipopolysaccharide (LPS)-binding effector TeoL and the outer membrane receptors CubA and CstR. We demonstrated that Cupriavidus necator T6SS1 secretes TeoL to preferentially associate with OMVs in the extracellular milieu through interactions with LPS, one of the most abundant components of OMVs. TeoL associated with OMVs can further bind outer membrane receptors CubA and CstR, which tethers OMVs to the recipient cells and allows cargo to be delivered. The LPS-mediated mechanism enables bacterial cells to recruit OMVs derived from different species, and confers advantages to bacterial cells in iron acquisition, interbacterial competition, and horizontal gene transfer (HGT). Moreover, our findings provide multiple new perspectives on T6SS functionality in the context of bacterial competition and HGT, through the recruitment of OMVs.

DNA binding by pilins and their interaction with the inner membrane platform of the DNA transporter in Thermus thermophilus

The natural transformation system of Thermus thermophilus has become a model system for studies of the structure and function of DNA transporter in thermophilic bacteria. The DNA transporter in T. thermophilus is functionally linked to type IV pili (T4P) and the major pilin PilA4 plays an essential role in both systems. However, T4P are dispensable for natural transformation. In addition to pilA4, T. thermophilus has a gene cluster encoding the three additional pilins PilA1-PilA3; deletion of the cluster abolished natural transformation but retained T4P biogenesis. In this study, we investigated the roles of single pilins PilA1, PilA2 and PilA3 in natural transformation by mutant studies. These studies revealed that each of these pilins is essential for natural transformation. Two of the pilins, PilA1 and PilA2, were found to bind dsDNA. PilA1 and PilA3 were detected in the inner membrane (IM) but not in the outer membrane (OM) whereas PilA2 was present in both membranes. All three pilins where absent in pilus fractions. This suggests that the pilins form a short DNA binding pseudopilus anchored in the IM. PilA1 was found to bind to the IM assembly platform of the DNA transporter via PilM and PilO. These data are in line with the hypothesis that a DNA binding pseudopilus is connected via an IM platform to the cytosolic motor ATPase PilF.

Pelzer B, Khodamoradi Y, Vehreschild MJGT. The role of the human gut microbiota in colonization and infection with multidrug-resistant bacteria

About 100 years ago, the first antibiotic drug was introduced into health care. Since then, antibiotics have made an outstanding impact on human medicine. However, our society increasingly suffers from collateral damage exerted by these highly effective drugs. The rise of resistant pathogen strains, combined with a reduction of microbiota diversity upon antibiotic treatment, has become a significant obstacle in the fight against invasive infections worldwide.Alternative and complementary strategies to classical "Fleming antibiotics" comprise microbiota-based treatments such as fecal microbiota transfer and administration of probiotics, live-biotherapeutics, prebiotics, and postbiotics. Other promising interventions, whose efficacy may also be influenced by the human microbiota, are phages and vaccines. They will facilitate antimicrobial stewardship, to date the only globally applied antibiotic resistance mitigation strategy.In this review, we present the available evidence on these nontraditional interventions, highlight their interaction with the human microbiota, and discuss their clinical applicability.

The ecological impact of a bacterial weapon: microbial interactions and the Type VI secretion system

Bacteria inhabit all known ecological niches and establish interactions with organisms from all kingdoms of life. These interactions are mediated by a wide variety of mechanisms and very often involve the secretion of diverse molecules from the bacterial cells. The Type VI secretion system (T6SS) is a bacterial protein secretion system that uses a bacteriophage-like machinery to secrete a diverse array of effectors, usually translocating them directly into neighbouring cells. These effectors display toxic activity in the recipient cell, making the T6SS an effective weapon during inter-bacterial competition and interactions with eukaryotic cells. Over the last two decades, microbiology research has experienced a shift towards using systems-based approaches to study the interactions between diverse organisms and their communities in an ecological context. Here, we focus on this aspect of the T6SS. We consider how our perspective of the T6SS has developed and examine what is currently known about the impact that bacteria deploying the T6SS can have in diverse environments, including niches associated with plants, insects and mammals. We consider how T6SS-mediated interactions can affect host organisms by shaping their microbiota, as well as the diverse interactions that can be established between different microorganisms through the deployment of this versatile secretion system.

Antimicrobial resistance acquisition via natural transformation: context is everything

Natural transformation is a process where bacterial cells actively take up free DNA from the environment and recombine it into their genome or reconvert it into extra-chromosomal genetic elements. Although this mechanism is known to mediate the uptake of antibiotic resistance determinants in a range of human pathogens, its importance in the spread of antimicrobial resistance is not always appreciated. This review highlights the context in which transformation takes place: in diverse microbiomes, in interaction with other forms of horizontal gene transfer and in increasingly polluted environments. This examination of the abiotic and biotic drivers of transformation reveals that it could be more important in the dissemination of resistance genes than is often recognised.

Formylglycine-generating enzyme-like proteins constitute a novel family of widespread type VI secretion system immunity proteins

Competition is a critical aspect of bacterial life, as it enables niche establishment and facilitates the acquisition of essential nutrients. Warfare between Gram-negative bacteria is largely mediated by the type VI secretion system (T6SS), a dynamic nanoweapon that delivers toxic effector proteins from an attacking cell to adjacent bacteria in a contact-dependent manner. Effector-encoding bacteria prevent self-intoxication and kin cell killing by the expression of immunity proteins, which prevent effector toxicity by specifically binding their cognate effector and either occluding its active site or preventing structural rearrangements necessary for effector activation. In this study, we investigate Tsi3, a previously uncharacterized T6SS immunity protein present in multiple strains of the human pathogen Acinetobacter baumannii. We show that Tsi3 is the cognate immunity protein of the antibacterial effector of unknown function Tse3. Our bioinformatic analyses indicate that Tsi3 homologs are widespread among Gram-negative bacteria, often encoded within T6SS effector-immunity modules. Surprisingly, we found that Tsi3 homologs are predicted to possess a characteristic formylglycine-generating enzyme (FGE) domain, which is present in various enzymatic proteins. Our data shows that Tsi3-mediated immunity is dependent on Tse3-Tsi3 protein-protein interactions and that Tsi3 homologs from various bacteria do not provide immunity against non-kin Tse3. Thus, we conclude that Tsi3 homologs are unlikely to be functional enzymes. Collectively, our work identifies FGE domain-containing proteins as important mediators of immunity against T6SS attacks and indicates that the FGE domain can be co-opted as a scaffold in multiple proteins to carry out diverse functions. Importance Despite the wealth of knowledge on the diversity of biochemical activities carried out by T6SS effectors, comparably little is known about the various strategies bacteria employ to prevent susceptibility to T6SS-dependent bacterial killing. Our work establishes a novel family of T6SS immunity proteins with a characteristic FGE domain. This domain is present in enzymatic proteins with various catalytic activities. Our characterization of Tsi3 expands the known functions carried out by FGE-like proteins to include defense during T6SS-mediated bacterial warfare. Moreover, it highlights the evolution of FGE domain-containing proteins to carry out diverse biological functions.

Driving to Safety: CRISPR-Based Genetic Approaches to Reducing Antibiotic Resistance

Bacterial resistance to antibiotics has reached critical levels, skyrocketing in hospitals and the environment and posing a major threat to global public health. The complex and challenging problem of reducing antibiotic resistance (AR) requires a network of both societal and science-based solutions to preserve the most lifesaving pharmaceutical intervention known to medicine. In addition to developing new classes of antibiotics, it is essential to safeguard the clinical efficacy of existing drugs. In this review, we examine the potential application of novel CRISPR-based genetic approaches to reducing AR in both environmental and clinical settings and prolonging the utility of vital antibiotics.

Price equation captures the role of drug interactions and collateral effects in the evolution of multidrug resistance

Bacterial adaptation to antibiotic combinations depends on the joint inhibitory effects of the two drugs (drug interaction [DI]) and how resistance to one drug impacts resistance to the other (collateral effects [CE]). Here we model these evolutionary dynamics on two-dimensional phenotype spaces that leverage scaling relations between the drug-response surfaces of drug-sensitive (ancestral) and drug-resistant (mutant) populations. We show that evolved resistance to the component drugs - and in turn, the adaptation of growth rate - is governed by a Price equation whose covariance terms encode geometric features of both the two-drug-response surface (DI) in ancestral cells and the correlations between resistance levels to those drugs (CE). Within this framework, mean evolutionary trajectories reduce to a type of weighted gradient dynamics, with the drug interaction dictating the shape of the underlying landscape and the collateral effects constraining the motion on those landscapes. We also demonstrate how constraints on available mutational pathways can be incorporated into the framework, adding a third key driver of evolution. Our results clarify the complex relationship between drug interactions and collateral effects in multidrug environments and illustrate how specific dosage combinations can shift the weighting of these two effects, leading to different and temporally explicit selective outcomes.

Acinetobacter defence mechanisms against biological aggressors and their use as alternative therapeutic applications

Several Acinetobacter strains are important nosocomial pathogens, with Acinetobacter baumannii being the species of greatest worldwide concern due to its multi-drug resistance and the recent appearance of hyper-virulent strains in the clinical setting. Colonisation of this environment is associated with a multitude of bacterial factors, and the molecular features that promote environmental persistence in abiotic surfaces, including intrinsic desiccation resistance, biofilm formation and motility, have been previously addressed. On the contrary, mechanisms enabling Acinetobacter spp. survival when faced against other biological competitors are starting to be characterised. Among them, secretion systems (SS) of different types, such as the T5bSS (Contact-dependent inhibition systems) and the T6SS, confer adaptive advantages against bacterial aggressors. Regarding mechanisms of defence against bacteriophages, such as toxin-antitoxin, restriction-modification, Crispr-Cas and CBASS, among others, have been identified but remain poorly characterised. In view of this, we aimed to summarise the present knowledge on defence mechanisms that enable niche establishment in members of the Acinetobacter genus. Different proposals are also described for the use of some components of these systems as molecular tools to treat Acinetobacter infections.

A novel stabilization mechanism for the type VI secretion system sheath

The T6SS is a microscopic harpoon that bacteria use to deliver toxins into neighboring cells. While its complex assembly process has been extensively studied, it remains unclear how the two forms (long and short) of the pivotal TssA protein affect T6SS function. TssA promotes baseplate formation, orchestrates sheath extension and, in its long form, interacts with a partner protein to anchor the extending sheath at the opposing side of the cell for up to 10 min. Here we demonstrate that short TssA proteins assist sheath stabilization by associating with a yet undescribed class of T6SS proteins that accumulate at the baseplate. These T6SSs fire in seconds; therefore, this discovery provides insight into the mechanism underpinning the different fighting strategies observed across T6SS-carrying bacteria.

The type VI secretion system (T6SS) is a phage-derived contractile nanomachine primarily involved in interbacterial competition. Its pivotal component, TssA, is indispensable for the assembly of the T6SS sheath structure, the contraction of which propels a payload of effector proteins into neighboring cells. Despite their key function, TssA proteins exhibit unexpected diversity and exist in two major forms, a short form (TssA_S) and a long form (TssA_L). While TssA_L proteins interact with a partner, called TagA, to anchor the distal end of the extended sheath, the mechanism for the stabilization of TssA_S-containing T6SSs remains unknown. Here we discover a class of structural components that interact with short TssA proteins and contribute to T6SS assembly by stabilizing the polymerizing sheath from the baseplate. We demonstrate that the presence of these components is important for full sheath extension and optimal firing. Moreover, we show that the pairing of each form of TssA with a different class of sheath stabilization proteins results in T6SS apparatuses that either reside in the cell for some time or fire immediately after sheath extension. We propose that this diversity in firing dynamics could contribute to the specialization of the T6SS to suit bacterial lifestyles in diverse environmental niches.

Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis

Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with activation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social interactions can override mechanistic barriers to horizontal gene transfer. We hypothesize that KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context.

Quantitative analysis of horizontal gene transfer in complex systems

Horizontal gene transfer (HGT) plays a significant role in rapidly propagating diverse traits throughout bacterial populations, thereby accelerating natural evolution and leading to complex community structures. Critical gene transfer rates underlying these occurrences dictate the efficiency and speed of gene spread; these rates are often highly specific to HGT mechanism and environmental context, and have historically been challenging to reliably quantify. In this review, we examine recent works that leverage rigorous quantitative methods to precisely measure these rates in a variety of settings beginning with in vitro studies and advancing to in situ measurements; we emphasize contexts where quantification across multiple scales of complexity has led to fundamental biological insights. Finally, we highlight the applications of these measurements and suggest potential methodological advances to improve our understanding.

Modular Molecular Weaponry Plays a Key Role in Competition Within an Environmental Vibrio cholerae Population

The type VI secretion system (T6SS) operons of Vibrio cholerae contain extraordinarily diverse arrays of toxic effector and cognate immunity genes, which are thought to play an important role in the environmental lifestyle and adaptation of this human pathogen. Through the T6SS, proteinaceous "spears" tipped with antibacterial effectors are injected into adjacent cells, killing those not possessing immunity proteins to these effectors. Here, we investigate the T6SS-mediated dynamics of bacterial competition within a single environmental population of V. cholerae. We show that numerous members of a North American V. cholerae population possess strain-specific repertoires of cytotoxic T6SS effector and immunity genes. Using pairwise competition assays, we demonstrate that the vast majority of T6SS-mediated duels end in stalemates between strains with different T6SS repertoires. However, horizontally acquired effector and immunity genes can significantly alter the outcome of these competitions. Frequently observed horizontal gene transfer events can both increase or reduce competition between distantly related strains by homogenizing or diversifying the T6SS repertoire. Our results also suggest temperature-dependent outcomes in T6SS competition, with environmental isolates faring better against a pathogenic strain under native conditions than under those resembling a host-associated environment. Taken altogether, these interactions produce density-dependent fitness effects and a constant T6SS-mediated arms race in individual V. cholerae populations, which could ultimately preserve intraspecies diversity. Since T6SSs are widespread, we expect within-population diversity in T6SS repertoires and the resulting competitive dynamics to be a common theme in bacterial species harboring this machinery.

Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters

Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar.

CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

Ecology and evolution of antimicrobial resistance in bacterial communities

Accumulating evidence suggests that the response of bacteria to antibiotics is significantly affected by the presence of other interacting microbes. These interactions are not typically accounted for when determining pathogen sensitivity to antibiotics. In this perspective, we argue that resistance and evolutionary responses to antibiotic treatments should not be considered only a trait of an individual bacteria species but also an emergent property of the microbial community in which pathogens are embedded. We outline how interspecies interactions can affect the responses of individual species and communities to antibiotic treatment, and how these responses could affect the strength of selection, potentially changing the trajectory of resistance evolution. Finally, we identify key areas of future research which will allow for a more complete understanding of antibiotic resistance in bacterial communities. We emphasise that acknowledging the ecological context, i.e. the interactions that occur between pathogens and within communities, could help the development of more efficient and effective antibiotic treatments.

Acinetobacter baylyi ADP1-naturally competent for synthetic biology

Acinetobacter baylyi ADP1 is a non-pathogenic soil bacterium known for its metabolic diversity and high natural transformation and recombination efficiency. For these features, A. baylyi ADP1 has been long exploited in studying bacterial genetics and metabolism. The large pool of information generated in the fundamental studies has facilitated the development of a broad range of sophisticated and robust tools for the genome and metabolic engineering of ADP1. This mini-review outlines and describes the recent advances in ADP1 engineering and tool development, exploited in, for example, pathway and enzyme evolution, genome reduction and stabilization, and for the production of native and non-native products in both pure and rationally designed multispecies cultures. The rapidly expanding toolbox together with the unique features of A. baylyi ADP1 provide a strong base for a microbial cell factory excelling in synthetic biology applications where evolution meets rational engineering.

Pilus Production in Acinetobacter baumannii Is Growth Phase Dependent and Essential for Natural Transformation

Rapid bacterial evolution has alarming negative impacts on animal and human health which can occur when pathogens acquire antimicrobial resistance traits. As a major cause of antibiotic-resistant opportunistic infections, A. baumannii is a high-priority health threat which has motivated renewed interest in studying how this pathogen acquires new, dangerous traits.

Acinetobacter baumannii is a severe threat to human health as a frequently multidrug-resistant hospital-acquired pathogen. Part of the danger from this bacterium comes from its genome plasticity and ability to evolve quickly by taking up and recombining external DNA into its own genome in a process called natural competence for transformation. This mode of horizontal gene transfer is one of the major ways that bacteria can acquire new antimicrobial resistances and toxic traits. Because these processes in A. baumannii are not well studied, we herein characterized new aspects of natural transformability in this species that include the species’ competence window. We uncovered a strong correlation with a growth phase-dependent synthesis of a type IV pilus (TFP), which constitutes the central part of competence-induced DNA uptake machinery. We used bacterial genetics and microscopy to demonstrate that the TFP is essential for the natural transformability and surface motility of A. baumannii, whereas pilus-unrelated proteins of the DNA uptake complex do not affect the motility phenotype. Furthermore, TFP biogenesis and assembly is subject to input from two regulatory systems that are homologous to Pseudomonas aeruginosa, namely, the PilSR two-component system and the Pil-Chp chemosensory system. We demonstrated that these systems affect not only the piliation status of cells but also their ability to take up DNA for transformation. Importantly, we report on discrepancies between TFP biogenesis and natural transformability within the same genus by comparing data for our work on A. baumannii to data reported for Acinetobacter baylyi, the latter of which served for decades as a model for natural competence.

IMPORTANCE Rapid bacterial evolution has alarming negative impacts on animal and human health which can occur when pathogens acquire antimicrobial resistance traits. As a major cause of antibiotic-resistant opportunistic infections, A. baumannii is a high-priority health threat which has motivated renewed interest in studying how this pathogen acquires new, dangerous traits. In this study, we deciphered a specific time window in which these bacteria can acquire new DNA and correlated that with its ability to produce the external appendages that contribute to the DNA acquisition process. These cell appendages function doubly for motility on surfaces and for DNA uptake. Collectively, we showed that A. baumannii is similar in its TFP production to Pseudomonas aeruginosa, though it differs from the well-studied species A. baylyi.