Dead cells release a 'necrosignal' that activates antibiotic survival pathways in bacterial swarms

Mechanisms conferring bacterial cell wall variability and adaptivity

The bacterial cell wall, a sophisticated and dynamic structure predominantly composed of peptidoglycan (PG), plays a pivotal role in bacterial survival and adaptation. Bacteria actively modify their cell walls by editing PG components in response to environmental challenges. Diverse variations in peptide composition, cross-linking patterns, and glycan strand structures empower bacteria to resist antibiotics, evade host immune detection, and adapt to dynamic environments. This review comprehensively summarizes the most common modifications reported to date and their associated adaptive role and further highlights how regulation of PG synthesis and turnover provides resilience to cell lysis.

Exposure to zinc and dialkyldimethyl ammonium compound alters bacterial community structure and resistance gene levels in partial sulfur autotrophic denitrification coupled with the Anammox process

Dialkyldimethyl ammonium compound (DADMAC) is widely used in daily life as a typical disinfectant and often co-exists with the heavy metal zinc in sewage environments. This study investigated the effects of co-exposure to zinc (1 mg/L) and DADMAC (0.2-5 mg/L) on the performance, bacterial community, and resistance genes (RGs) in a partial sulfur autotrophic denitrification coupled with anaerobic ammonium oxidation (PSAD-Anammox) system in a sequencing batch moving bed biofilm reactor for 150 days. Co-exposure to zinc and low concentration (0.2 mg/L) DADMAC did not affect the nitrogen removal ability of the PASD-Anammox system, but increased the abundance and transmission risk of free RGs in water. Co-exposure to zinc and medium-to-high (2-5 mg/L) DADMAC led to fluctuations in and inhibition of nitrogen removal, which might be related to the enrichment of heterotrophic denitrifying bacteria dominated by Denitratisoma. Co-exposure to zinc and high concentration DADMAC (5 mg/L) stimulated the secretion of extracellular polymeric substances and increased the proliferation risk of intracellular RGs in sludge. This study provided insights into the application of PSAD-Anammox system and the ecological risks of wastewater containing zinc and DADMAC.

Deciphering the influence of NaCl on social behaviour of Bacillus subtilis

Various environmental signals, such as temperature, pH, nutrient levels, salt content and the presence of other microorganisms, can influence biofilm's development and dynamics. However, the innate mechanisms that govern at the molecular and cellular levels remain elusive. Here, we report the impact of physiologically relevant concentrations of NaCl on biofilm formation and the associated differences in an undomesticated natural isolate of Bacillus subtilis. NaCl exposure and its uptake by bacterial cells induced substantial changes in the architecture of pellicle biofilm and an upsurge in the expansion of biofilm colonies on agar surfaces. We have observed the upregulation of genes involved in motility and the downregulation of genes involved in the biosynthesis of extracellular matrix components through the transcription factor sigD, suggesting the possible underlying mechanisms. To further support these observations, we have used ΔsigD and ΔsrfAC null mutants, which showed compromised NaCl-induced effects. Our results indicate that NaCl induces a lifestyle shift in B. subtilis from a sessile biofilm state to an independent unicellular motile state. Overall, we present evidence that NaCl can reprogramme gene expression and alter cellular morphology and the state of cells to adapt to motility, which facilitates the expansion of bacterial colonies.

Flagellar protein FliL: A many-splendored thing

FliL is a bacterial flagellar protein demonstrated to associate with, and regulate ion flow through, the stator complex in a diverse array of bacterial species. FliL is also implicated in additional functions such as stabilizing the flagellar rod, modulating rotor bias, sensing the surface, and regulating gene expression. How can one protein do so many things? Its location is paramount to understanding its numerous functions. This review will look at the evidence, attempt to resolve some conflicting findings, and offer new thoughts on FliL.

How Bacteria Cope with Oxidative Stress Induced by Cadmium: Volatile Communication Is Differentially Perceived among Strains

Soil is an environment with numerous niches, where bacteria are exposed to diverse conditions. Some bacteria are exposed earlier than others to pressure, and the emission of signals that other bacteria can receive and perceive may allow a better response to an eminent stimulus. To shed light on how bacteria trigger their response and adapt to changes in the environment, the intra- and interspecific influences of volatiles on bacterial strains growing under non-stressed and cadmium-stressed conditions were assessed. Each strain was exposed to its volatiles emitted by cells growing under different conditions to test whether the environment in which a cell grows influences neighboring cells. The five genera tested showed different responses, with Rhizobium displaying the greatest influence. In a second experiment, 13 strains from different genera were grown under control conditions but exposed to volatiles released by Cd-stressed Rhizobium cells to ascertain whether Rhizobium's observed influence was strain-specific or broader. Our results showed that the volatiles emitted by some bacteria under stress are differentially perceived and translated into biochemical changes (growth, alteration of the antioxidant response, and oxidative damage) by other bacteria, which may increase the adaptability and resilience of bacterial communities to environmental changes, especially those with a prooxidant nature. Cadmium (Cd) contamination of soils constitutes a risk to the environment and human health. Here, we showed the effects of Cd exposure on bacteria and how volatile communication influences the biochemistry related to coping with oxidative stress. This knowledge can be important for remediation and risk assessment and highlights that new biological features, such as volatile communication, should be considered when studying and assessing the impact of contaminants on soil ecosystems.

A new understanding on the prerequisite of antibiotic biodegradation in wastewater treatment: Adhesive behavior between antibiotic-degrading bacteria and ciprofloxacin

The extensive exploration of antibiotic biodegradation by antibiotic-degrading bacteria in biological wastewater treatment processes has left a notable gap in understanding the behavior of these bacteria when exposed to antibiotics and the initiation of biodegradation processes. This study, therefore, delves into the adhesive behavior of Paraclostridium bifermentans, isolated from a bioreactor treating ciprofloxacin-laden wastewater, towards ciprofloxacin molecules. For the first time, this behavior is observed and characterized through quartz crystal microbalance with dissipation (QCM-D) and atomic force microscopy. The investigation further extends to identify key regulatory factors and mechanisms governing this adhesive behavior through a comparative proteomics analysis. The results reveal the dominance of extracellular proteins, particularly those involved in nucleotide binding, hydrolase, and transferase, in the adhesion process. These proteins play pivotal roles through direct chemical binding and the regulation of signaling molecule. Furthermore, QCM-D measurements provide evidence that transferase-related signaling molecules, especially tyrosine, augment the binding between ciprofloxacin and transferases, resulting in enhance ciprofloxacin removal by P. bifermentans (increased by ∼1.2-fold). This suggests a role for transferase-related signaling molecules in manipulating the adhesive behavior of P. bifermentans towards ciprofloxacin. These findings contribute to a new understanding of the prerequisites for antibiotic biodegradation and offer potential strategies for improving the application of antibiotic-degrading bacteria in the treatment of antibiotics-laden wastewater.

Influence of Dead Cells Killed by Industrial Biocides (BAC and DBNPA) on Biofilm Formation

Industrial biocides aim to keep water systems microbiologically controlled and to minimize biofouling. However, the resulting dead cells are usually not removed from the water streams and can influence the growth of the remaining live cells in planktonic and sessile states. This study aims to understand the effect of dead Pseudomonas fluorescens cells killed by industrial biocides-benzalkonium chloride (BAC) and 2,2-dibromo-3-nitrilopropionamide (DBNPA)-on biofilm formation. Additionally, the effect of different dead/live cell ratios (50.00% and 99.99%) was studied. The inoculum was recirculated in a Parallel Plate Flow Cell (PPFC). The overall results indicate that dead cells greatly affect biofilm properties. Inoculum with DBNPA-dead cells led to more active (higher ATP content and metabolic activity) and thicker biofilm layers in comparison to BAC-dead cells, which seems to be linked to the mechanism of action by which the cells were killed. Furthermore, higher dead cell ratios (99.99%) in the inoculum led to more active (higher culturability, metabolic activity and ATP content) and cohesive/compact and uniformly distributed biofilms in comparison with the 50.00% dead cell ratio. The design of future disinfection strategies must consider the contribution of dead cells to the biofilm build-up, as they might negatively affect water system operations.

Targeted phytogenic compounds against Vibrio parahaemolyticus biofilms

As one of main culprit of seafood-associated human illness, Vibrio parahaemolyticus can readily accumulate on biotic or abiotic surfaces to form biofilms in the seafood processing environment. Biofilm formation on various surfaces can provide a protective barrier for viable bacterial cells that are resistant to most traditional bacteriostatic measures. This underscores the necessity and urgency of developing effective alternative strategies to control V. parahaemolyticus biofilms. Plants have always provided an extensive and infinite source of biologically active compounds for "green" antibiofilm agents. This review summarizes recent developments in promising multitargeted phytogenic compounds against V. parahaemolyticus biofilms. This review provides valuable insights into potential research targets that can be pursued further to identify potent natural antibiofilm agents in the food industry.

A heritable iron memory enables decision-making in Escherichia coli

The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when Escherichia coli encounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This "iron" memory preexists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, which tracks with its iron memory, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We demonstrate that cellular iron levels also track with biofilm formation and antibiotic tolerance, suggesting that iron memory may impact other physiologies.

Polycation-Intercalated MXene Membrane with Enhanced Permselective and Anti-Microbial Properties

Two-dimensional (2D) nanomaterial-based membranes feature attractive properties for molecular separation and transport, which exhibit huge potential in various chemical processes. However, the low permeability and bio-fouling of the MXene membrane in water treatment become huge obstacles to its practical application. Herein, a highly permselective and anti-bacterial 2D nanofiltration membrane is fabricated by intercalating a polycation of polydiallyldimethylammonium chloride (PDDA) into the Ti3C2Tx MXene laminar architecture through a facile and patternable electrostatic assembly strategy. As a result, the as-fabricated Ti3C2Tx/PDDA composite membrane exhibits higher water permeance up to 73.4 L m-2 h-1 with a rejection above 94.6% for MgCl2. The resultant membrane simultaneously possesses good resistance to swelling and long-term stability in water environments, even after 8 h. Additionally, the Ti3C2Tx/PDDA membrane also demonstrates a high flux recovery ratio of nearly 96.1% to bovine serum albumin proteins after being cleaned. More importantly, the current membrane shows excellent anti-adhesive and anti-microbial activity against Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus), with inhibition rates of 90% and 95% against E. coli and S. aureus, respectively. This holds great potential for the application of the polyelectrolyte-intercalated MXene membrane in serving as a promising platform to separate molecules and/or ions in an aquatic environment.

Bacterial motility can govern the dynamics of antibiotic resistance evolution

Spatial heterogeneity in antibiotic concentrations is thought to accelerate the evolution of antibiotic resistance, but current theory and experiments have overlooked the effect of cell motility on bacterial adaptation. Here, we study bacterial evolution in antibiotic landscapes with a quantitative model where bacteria evolve under the stochastic processes of proliferation, death, mutation and migration. Numerical and analytical results show that cell motility can both accelerate and decelerate bacterial adaptation by affecting the degree of genotypic mixing and ecological competition. Moreover, we find that for sufficiently high rates, cell motility can limit bacterial survival, and we derive conditions for all these regimes. Similar patterns are observed in more complex scenarios, namely where bacteria can bias their motion in chemical gradients (chemotaxis) or switch between motility phenotypes either stochastically or in a density-dependent manner. Overall, our work reveals limits to bacterial adaptation in antibiotic landscapes that are set by cell motility.

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli, AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

Flagellar motor remodeling during swarming requires FliL

FliL is an essential component of the flagellar machinery in some bacteria, but a conditional one in others. The conditional role is for optimal swarming in some bacteria. During swarming, physical forces associated with movement on a surface are expected to exert a higher load on the flagellum, requiring more motor torque to move. Bacterial physiology and morphology are also altered during swarming to cope with the challenges of surface navigation. FliL was reported to enhance motor output in several bacteria and observed to assemble as a ring around ion-conducting stators that power the motor. In this study we identify a common new function for FliL in diverse bacteria - Escherichia coli, Bacillus subtilis and Proteus mirabilis . During swarming, all these bacteria show increased cell speed and a skewed motor bias that suppresses cell tumbling. We demonstrate that these altered motor parameters, or 'motor remodeling', require FliL. Both swarming and motor remodeling can be restored in an E. coli fliL mutant by complementation with fliL genes from P. mirabilis and B. subtilis , showing conservation of swarming-associated FliL function across phyla. In addition, we demonstrate that the strong interaction we reported earlier between FliL and the flagellar MS-ring protein FliF is confined to the RBM-3 domain of FliF that links the periplasmic rod to the cytoplasmic C-ring. This interaction may explain several phenotypes associated with the absence of FliL.

Iron Memory in E. coli

The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when E. coli encounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This memory pre-exists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, whether low or high, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We also demonstrate that iron memory can integrate multiple stimuli, impacting other bacterial behaviors such as biofilm formation and antibiotic tolerance.

Polyamines and linear DNA mediate bacterial threat assessment of bacteriophage infection

Monitoring the extracellular environment for danger signals is a critical aspect of cellular survival. However, the danger signals released by dying bacteria and the mechanisms bacteria use for threat assessment remain largely unexplored. Here, we show that lysis of Pseudomonas aeruginosa cells releases polyamines that are subsequently taken up by surviving cells via a mechanism that relies on Gac/Rsm signaling. While intracellular polyamines spike in surviving cells, the duration of this spike varies according to the infection status of the cell. In bacteriophage-infected cells, intracellular polyamines are maintained at high levels, which inhibits replication of the bacteriophage genome. Many bacteriophages package linear DNA genomes and linear DNA is sufficient to trigger intracellular polyamine accumulation, suggesting that linear DNA is sensed as a second danger signal. Collectively, these results demonstrate how polyamines released by dying cells together with linear DNA allow P. aeruginosa to make threat assessments of cellular injury.

Swarming Motility Assays in Salmonella

Salmonella enterica has six subspecies, of which the subspecies enterica is the most important for human health. The dispersal and infectivity of this species are dependent upon flagella-driven motility. Two kinds of flagella-mediated movements have been described-swimming individually in bulk liquid and swarming collectively over a surface substrate. During swarming, the bacteria acquire a distinct physiology, the most significant consequence of which is acquisition of adaptive resistance to antibiotics. Described here are protocols to cultivate, verify, and study swimming and swarming motility in S. enterica, and an additional "border-crossing" assay, where cells "primed" to swarm are presented with an environmental challenge such as antibiotics to assess their propensity to handle the challenge.

Therapeutic potential of otilonium bromide against Vibrio vulnificus

New drugs are urgently required for the treatment of infections due to an increasing number of new strains of diseases-causing pathogens and antibiotic-resistant bacteria. A library of drugs approved by Food and Drug Administration was screened for efficacy against Vibrio vulnificus using antimicrobial assays. We found that otilonium bromide showed potent antimicrobial activity against V.vulnificus and had a synergistic effect in combination with antibiotics. Field emission transmission electron microscope images revealed that otilonium bromide caused cell division defects in V.vulnificus. Moreover, it significantly inhibited V.vulnificus swarming motility and adhesion to host cells at concentrations lower than the minimum inhibitory concentration. To investigate its inhibitory action mechanisms, we examined the effect of otilonium bromide on the expression levels of several proteins crucial for V.vulnificus growth, motility, and adhesion. It decreased the protein expression levels of cAMP receptor protein and flagellin B, but not HlyU or OmpU. In addition, otilonium bromide significantly decreased the expression levels of outer membrane protein TolCV1, thus inhibiting RtxA1 toxin secretion and substantially reducing V.vulnificus cytotoxicity to host cells. Collectively, these findings suggest that otilonium bromide may be considered as a promising candidate for treating V.vulnificus infections.

Role of Dead Cells in Collective Stress Tolerance in Microbial Communities: Evidence from Yeast

A substantial part of yeast life cycle takes place in the communities where the cells are surrounded by their own clones. Meanwhile, yeast cell fitness depends not only on its own adaptations but also on the processes in the neighboring cells. Moreover, even if a cell loses its clonogenic ability, it is still capable of protecting surrounding cells that are still alive. Dead cells can absorb lipophilic antibiotics and provide nutrients to their kin neighbors. Some enzymes can be released into the environment and detoxify exogenous toxins. For example, cytosolic catalase, which degrades hydrogen peroxide, can stay active outside of the cell. Inviable cells of pathogenic yeast species can suppress host immune responses and, in this way, boost spread of the pathogen. In this review, we speculate that biochemical processes in dying cells can facilitate increase of stress resistance in the alive kin cells and therefore be a subject of natural selection. We considered possible scenarios of how dead microbial cells can increase survival of their kin using unicellular fungi - baker's yeast Saccharomyces cerevisiae - as an example. We conclude that the evolutionary conserved mechanisms of programmed cell death in yeast are likely to include a module of early permeabilization of the cell plasma membrane rather than preserve its integrity.

Efflux-linked accelerated evolution of antibiotic resistance at a population edge

Efflux is a common mechanism of resistance to antibiotics. We show that efflux itself promotes accumulation of antibiotic-resistance mutations (ARMs). This phenomenon was initially discovered in a bacterial swarm where the linked phenotypes of high efflux and high mutation frequencies spatially segregated to the edge, driven there by motility. We have uncovered and validated a global regulatory network connecting high efflux to downregulation of specific DNA-repair pathways even in non-swarming states. The efflux-DNA repair link was corroborated in a clinical "resistome" database: genomes with mutations that increase efflux exhibit a significant increase in ARMs. Accordingly, efflux inhibitors decreased evolvability to antibiotic resistance. Swarms also revealed how bacterial populations serve as a reservoir of ARMs even in the absence of antibiotic selection pressure. High efflux at the edge births mutants that, despite compromised fitness, survive there because of reduced competition. This finding is relevant to biofilms where efflux activity is high.

Bio-Inspired Self-Adaptive Nanocomposite Array: From Non-antibiotic Antibacterial Actions to Cell Proliferation

Pathogenic bacterial infection and poor native tissue integration are two major issues encountered by biomaterial implants and devices, which are extremely hard to overcome within a single surface, especially for those without involvement of antibiotics. Herein, a self-adaptive surface that can transform from non-antibiotic antibacterial actions to promotion of cell proliferation is developed by in situ assembly of bacteriostatic 3,3'-diaminodipropylamine (DADP)-doped zeolitic imidazolate framework-8 (ZIF-8) on bio-inspired nanopillars. Initially, the nanocomposite surface shows impressive antibacterial effects, even under severe bacterial infection, due to the combination of mechano-bactericidal activity from a nanopillar structure and bacteriostatic activity contributed by pH-responsive release of DADP. After the complete degradation of the ZIF-8 layer, the refurbished nanopillars not only can still physically rupture bacterial membrane but also facilitate mammalian cell proliferation, due to the obvious difference in cell size. More strikingly, the nanocomposite surface totally avoids the usage of antibiotics, eradicating the potential risk of antimicrobial resistance, and the surface exhibited excellent histocompatibility and lower inflammatory response properties as revealed by in vivo tests. This type of self-adaptive surface may provide a promising alternative for addressing the intractable implant-associated requirements, where antibiotic-free antibacterial activity and native tissue integration are both highly needed.

Modification of ultrafiltration membrane with antibacterial agent intercalated layered nanosheets: Toward superior antibiofouling performance for water treatment

Membrane fouling, especially biofouling induced by biofilm formation on membranes, can result in frequent cleaning or even replacement of membranes. Fabrication of membrane with excellent antibiofouling property is quite attractive due to its effectiveness and low-impact on the operation of membrane-based process. Herein, a cationic antibacterial agent, quaternary ammonium compound (QAC), was intercalated into the interlayer spaces of the MgAl layered double hydroxide (QAC/LDH) by self-assembly. The QAC/LDH composite was incorporated into polyethersulfone (PES) ultrafiltration (UF) membrane (PES-QLDH). The QAC/LDH enhanced the hydrophilicity, water flux, and resistance to organic fouling for the PES-QLDH membrane. The PES-QLDH membrane exhibited superior antibiofouling performance than the control PES membrane, with deposition of a thinner biofilm layer consisted of almost dead cells. The superior antibacterial activity inhibits the adhesion and growth of bacteria on the membrane surface, effectively retarding the formation of biofilms. Importantly, the synergistic effect of QAC and LDH in the PES-QLDH membrane resulted in a high biocidal activity based on both direct and indirect killing mechanisms. The PES-QLDH membrane maintained a stable and high antibacterial activity after several fouling-cleaning cycles. These results imply that the PES-QLDH membrane provides an effective and promising strategy for its long-term application in wastewater treatment.

Inhibition of citral nanoemulsion to growth, spoilage ability and AI-2/luxS quorum sensing system of Shewanella putrefaciens CN-32: A study on bacteriostasis from in vitro culture and gene expression analysis

Objectives

The bacteriostatic effects of a citral nanoemulsion against Shewanella putrefaciens CN-32 (SHP CN-32) were investigated using in vitro culture and gene expression analysis, for building a potential application in spoilage microorganism control and aquatic products quality maintenance.

Materials and Methods

The SHP CN-32 was treated by prepared citral nanoemulsion when the minimal inhibitory concentration (MIC) was verified. The growth curve, membrane integrity, scanning electron microscope (SEM) observation, biofilm formation and quorum sensing (QS) signaling molecule AI-2 content were evaluated in different MIC treatment groups (0 MIC to 1.00 MIC). The gene expression status of SHP CN-32 in 0 MIC group and 0.50 MIC group were compared using transcriptome sequencing and quantitative PCR.

Results

The in vitro culture revealed that the citral nanoemulsion could inhibit the growth of SHP CN-32 with MIC of about 200 μg/ml. Images from membrane integrity, SEM and biofilm formation suggested significant biological structure damage in bacteria after treatment. Meanwhile, the quorum sensing (QS) signaling molecule AI-2 content showed a decline following the rise of treatment concentration. Transcriptome sequencing and quantitative PCR revealed that the majority genes related diversified functional metabolic pathways of SHP CN-32 were down-regulated at varying degree.

Conclusion

A significant bacteriostasis of citral nanoemulsion against Shewanella putrefaciens CN-32 (SHP CN-32) were verified via the results of growth inhibition, structural destruction, signal molecular decrease and gene expression down-regulation of strains. These synergies significantly affect the characteristic expression of SHP CN-32, revealing the application potential as bacteriostat, QS inhibitor and preservative in aquatic products.

MDR Pumps as Crossroads of Resistance: Antibiotics and Bacteriophages

At present, antibiotic resistance represents a global problem in modern medicine. In the near future, humanity may face a situation where medicine will be powerless against resistant bacteria and a post-antibiotic era will come. The development of new antibiotics is either very expensive or ineffective due to rapidly developing bacterial resistance. The need to develop alternative approaches to the treatment of bacterial infections, such as phage therapy, is beyond doubt. The cornerstone of bacterial defense against antibiotics are multidrug resistance (MDR) pumps, which are involved in antibiotic resistance, toxin export, biofilm, and persister cell formation. MDR pumps are the primary non-specific defense of bacteria against antibiotics, while drug target modification, drug inactivation, target switching, and target sequestration are the second, specific line of their defense. All bacteria have MDR pumps, and bacteriophages have evolved along with them and use the bacteria’s need for MDR pumps to bind and penetrate into bacterial cells. The study and understanding of the mechanisms of the pumps and their contribution to the overall resistance and to the sensitivity to bacteriophages will allow us to either seriously delay the onset of the post-antibiotic era or even prevent it altogether due to phage-antibiotic synergy.

Biocompatible mechano-bactericidal nanopatterned surfaces with salt-responsive bacterial release

Bio-inspired nanostructures have demonstrated highly efficient mechano-bactericidal performances with no risk of bacterial resistance; however, they are prone to become contaminated with the killed bacterial debris. Herein, a biocompatible mechano-bactericidal nanopatterned surface with salt-responsive bacterial releasing behavior is developed by grafting salt-responsive polyzwitterionic (polyDVBAPS) brushes on a bio-inspired nanopattern surface. Benefiting from the salt-triggered configuration change of the grafted polymer brushes, this dual-functional surface shows high mechano-bactericidal efficiency in water (low ionic strength condition), while the dead bacterial residuals can be easily lifted by the extended polymer chains and removed from the surface in 1 M NaCl solution (high ionic strength conditions). Notably, this functionalized nanopatterned surface shows selective biocidal activity between bacterial cells sand eukaryotic cells. The biocompatibility with red blood cells (RBCs) and mammalian cells was tested in vitro. The histocompatibility and prevention of perioperative contamination activity were verified by in vivo evaluation in a rat subcutaneous implant model. This nanopatterned surface with bacterial killing and releasing activities may open new avenues for designing bio-inspired mechano-bactericidal platforms with long-term efficacy, thus presenting a facile alternative in combating perioperative-related bacterial infection. STATEMENT OF SIGNIFICANCE: Bioinspired nanostructured surfaces with noticeable mechano-bactericidal activity showed great potential in moderating drug-resistance. However, the nanopatterned surfaces are prone to be contaminated by the killed bacterial debris and compromised the bactericidal performance. In this study, we provide a dual-functional antibacterial conception with both mechano-bactericidal and bacterial releasing performances not requiring external chemical bactericidal agents. Additionally, this functionalized antibacterial surface also shows selective biocidal activity between bacteria and eukaryotic cells, and the excellent biocompatibility was tested in vitro and in vivo. The new concept for the functionalized mechano-bactericidal surface here illustrated presents a facile antibiotic-free alternative in combating perioperative related bacterial infection in practical application.

Positively-charged microcrystalline cellulose microparticles: Rapid killing effect on bacteria, trapping behavior and excellent elimination efficiency of biofilm matrix from water environment

Pathogen and biofilm contamination in aqueous systems leave millions of people at risk of waterborne diseases. Herein, to address this issue, a green and highly efficient strategy is developed to concurrently trap and kill bacteria, eliminate the debris and the existing biofilm matrix in water environment via magnetic microparticles. The particles (TPFPs) were prepared from the in-situ deposition of Fe₃O₄ nanoparticles onto the surface of antibacterial functionalized microcrystalline cellulose (MCC). Noticeably, TPFPs can completely inactivate both S. aureus and E. coli once contacting for 30 min by disrupting the bacterial membrane. Meanwhile, the MCC-based magnetic particles retained 100% biocidal efficiency against E. coli (5 * 10⁴E. coli/mg particles) during ten recycling procedures without any treatment. More importantly, according to the results of trapping behavior and antibiofilm assays, not only bacteria could be captured by the particles (trapping rate was over 85%), but also the residual debris from dead bacteria and fragmented biofilm was together removed based on the special structure and functions of the antibacterial particles (~ 80%), including extremely rough surfaces, surficial positive charge and magneto-responsive property. This study presents an efficient approach for microorganism management in water system which can be expectantly applied to improve the water safety.

Exposure to lysed bacteria can promote or inhibit growth of neighbouring live bacteria depending on local abiotic conditions

Microbial death is extremely common in nature, yet the ecological role of dead bacteria is unclear. Dead cells are assumed to provide nutrients to surrounding microbes, but may also affect them in other ways. We found adding lysate prepared from dead bacteria to cultures of E. coli in nutrient-rich conditions suppressed their final population density. This is in stark contrast with the notion that the primary role of dead cells is nutritional, although we also observed this type of effect when we added dead bacteria to cultures that were not supplied with other nutrients. We only observed the growth-suppressive effect of our dead-bacteria treatment after they had undergone significant lysis, suggesting a key role for cellular contents released during lysis. Transcriptomic analysis indicated changes in gene expression in response to dead cells in growing populations, particularly in genes involved in motility. This was supported by experiments with genetic knockouts and copy-number manipulation. Because lysis is commonplace in natural and clinical settings, the growth-suppressive effect of dead cells we describe here may be a widespread and previously unrecognized constraint on bacterial population growth.

Messages from the dead protect bacteria from viral attack

Bacterial populations are ubiquitously threatened by viral predation. In this issue, Tzipilevich and colleagues show that bacteria killed by viruses release a danger signal that warns neighboring cells to ramp up their defenses. This "message from the dead" thereby induces phenotypic tolerance to infections and slows down viral spread in the population.

Multidrug Resistance Pumps as a Keystone of Bacterial Resistance

Antibiotic resistance is a global problem of modern medicine. A harbinger of the onset of the postantibiotic era is the complexity and high cost of developing new antibiotics as well as their inefficiency due to the rapidly developing resistance of bacteria. Multidrug resistance (MDR) pumps, involved in the formation of resistance to xenobiotics, the export of toxins, the maintenance of cellular homeostasis, and the formation of biofilms and persistent cells, are the keystone of bacterial protection against antibiotics. MDR pumps are the basis for the nonspecific protection of bacteria, while modification of the drug target, inactivation of the drug, and switching of the target or sequestration of the target is the second specific line of their protection. Thus, the nonspecific protection of bacteria formed by MDR pumps is a barrier that prevents the penetration of antibacterial substances into the cell, which is the main factor determining the resistance of bacteria. Understanding the mechanisms of MDR pumps and a balanced assessment of their contribution to total resistance, as well as to antibiotic sensitivity, will either seriously delay the onset of the postantibiotic era or prevent its onset in the foreseeable future.

A Model for Allosteric Communication in Drug Transport by the AcrAB-TolC Tripartite Efflux Pump

RND family efflux pumps are complex macromolecular machines involved in multidrug resistance by extruding antibiotics from the cell. While structural studies and molecular dynamics simulations have provided insights into the architecture and conformational states of the pumps, the path followed by conformational changes from the inner membrane protein (IMP) to the periplasmic membrane fusion protein (MFP) and to the outer membrane protein (OMP) in tripartite efflux assemblies is not fully understood. Here, we investigated AcrAB-TolC efflux pump's allostery by comparing resting and transport states using difference distance matrices supplemented with evolutionary couplings data and buried surface area measurements. Our analysis indicated that substrate binding by the IMP triggers quaternary level conformational changes in the MFP, which induce OMP to switch from the closed state to the open state, accompanied by a considerable increase in the interface area between the MFP subunits and between the OMPs and MFPs. This suggests that the pump's transport-ready state is at a more favourable energy level than the resting state, but raises the puzzle of how the pump does not become stably trapped in a transport-intermediate state. We propose a model for pump allostery that includes a downhill energetic transition process from a proposed 'activated' transport state back to the resting pump.

Surveying a Swarm: Experimental Techniques to Establish and Examine Bacterial Collective Motion

The survival and successful spread of many bacterial species hinges on their mode of motility. One of the most distinct of these is swarming, a collective form of motility where a dense consortium of bacteria employ flagella to propel themselves across a solid surface. Surface environments pose unique challenges, derived from higher surface friction/tension and insufficient hydration. Bacteria have adapted by deploying an array of mechanisms to overcome these challenges. Beyond allowing bacteria to colonize new terrain in the absence of bulk liquid, swarming also bestows faster speeds and enhanced antibiotic resistance to the collective. These crucial attributes contribute to the dissemination, and in some cases pathogenicity, of an array of bacteria. This mini-review highlights; 1) aspects of swarming motility that differentiates it from other methods of bacterial locomotion. 2) Facilitatory mechanisms deployed by diverse bacteria to overcome different surface challenges. 3) The (often difficult) approaches required to cultivate genuine swarmers. 4) The methods available to observe and assess the various facets of this collective motion, as well as the features exhibited by the population as a whole.

Adaptive Role of Cell Death in Yeast Communities Stressed with Macrolide Antifungals

Microorganisms cooperate with each other to protect themselves from environmental stressors. An extreme case of such cooperation is regulated cell death for the benefit of other cells. Dying cells can provide surviving cells with nutrients or induce their stress response by transmitting an alarm signal; however, the role of dead cells in microbial communities is unclear. Here, we searched for types of stressors the protection from which can be achieved by death of a subpopulation of cells. Thus, we compared the survival of Saccharomyces cerevisiae cells upon exposure to various stressors in the presence of additionally supplemented living versus dead cells. We found that dead cells contribute to yeast community resistance against macrolide antifungals (e.g., amphotericin B [AmB] and filipin) to a greater extent than living cells. Dead yeast cells absorbed more macrolide filipin than control cells because they exposed intracellular sterol-rich membranes. We also showed that, upon the addition of lethal concentrations of AmB, supplementation with AmB-sensitive cells but not with AmB-resistant cells enabled the survival of wild-type cells. Together, our data suggest that cell-to-cell heterogeneity in sensitivity to AmB can be an adaptive mechanism helping yeast communities to resist macrolides, which are naturally occurring antifungal agents.

IMPORTANCE Eukaryotic microorganisms harbor elements of programmed cell death (PCD) mechanisms that are homologous to the PCD of multicellular metazoa. However, it is still debated whether microbial PCD has an adaptive role or whether the processes of cell death are an aimless operation in self-regulating molecular mechanisms. Here, we demonstrated that dying yeast cells provide an instant benefit for their community by absorbing macrolides, which are bacterium-derived antifungals. Our results illustrate the principle that the death of a microorganism can contribute to the survival of its kin and suggest that early plasma membrane permeabilization improves community-level protection. The latter makes a striking contrast to the manifestations of apoptosis in higher eukaryotes, the process by which plasma membranes maintain integrity.

TolCV1 Has Multifaceted Roles During Vibrio vulnificus Infection

RtxA1 is a major cytotoxin of Vibrio vulnificus (V. vulnificus) causing fatal septicemia and necrotic wound infections. Our previous work has shown that RpoS regulates the expression and secretion of V. vulnificus RtxA1 toxin. This study was conducted to further investigate the potential mechanisms of RpoS on RtxA1 secretion. First, V. vulnificus TolCV1 and TolCV2 proteins, two Escherichia coli TolC homologs, were measured at various time points by Western blotting. The expression of TolCV1 was increased time-dependently, whereas that of TolCV2 was decreased. Expression of both TolCV1 and TolCV2 was significantly downregulated in an rpoS deletion mutation. Subsequently, we explored the roles of TolCV1 and TolCV2 in V. vulnificus pathogenesis. Western blot analysis showed that RtxA1 toxin was exported by TolCV1, not TolCV2, which was consistent with the cytotoxicity results. Furthermore, the expression of TolCV1 and TolCV2 was increased after treatment of the host signal bile salt and the growth of tolCV1 mutant was totally abolished in the presence of bile salt. A tolCV1 mutation resulted in significant reduction of V. vulnificus induced-virulence in mice. Taken together, TolCV1 plays key roles in RtxA1 secretion, bile salt resistance, and mice lethality of V. vulnificus, suggesting that TolCV1 could be an attractive target for the design of new medicines to treat V. vulnificus infections.

Cytochrome bd promotes Escherichia coli biofilm antibiotic tolerance by regulating accumulation of noxious chemicals

Nutrient gradients in biofilms cause bacteria to organize into metabolically versatile communities capable of withstanding threats from external agents including bacteriophages, phagocytes, and antibiotics. We previously determined that oxygen availability spatially organizes respiration in uropathogenic Escherichia coli biofilms, and that the high-affinity respiratory quinol oxidase cytochrome bd is necessary for extracellular matrix production and biofilm development. In this study we investigate the physiologic consequences of cytochrome bd deficiency in biofilms and determine that loss of cytochrome bd induces a biofilm-specific increase in expression of general diffusion porins, leading to elevated outer membrane permeability. In addition, loss of cytochrome bd impedes the proton mediated efflux of noxious chemicals by diminishing respiratory flux. As a result, loss of cytochrome bd enhances cellular accumulation of noxious chemicals and increases biofilm susceptibility to antibiotics. These results identify an undescribed link between E. coli biofilm respiration and stress tolerance, while suggesting the possibility of inhibiting cytochrome bd as an antibiofilm therapeutic approach.

The role of the microbiome in ovarian cancer: mechanistic insights into oncobiosis and to bacterial metabolite signaling

Ovarian cancer is characterized by dysbiosis, referred to as oncobiosis in neoplastic diseases. In ovarian cancer, oncobiosis was identified in numerous compartments, including the tumor tissue itself, the upper and lower female genital tract, serum, peritoneum, and the intestines. Colonization was linked to Gram-negative bacteria with high inflammatory potential. Local inflammation probably participates in the initiation and continuation of carcinogenesis. Furthermore, local bacterial colonies in the peritoneum may facilitate metastasis formation in ovarian cancer. Vaginal infections (e.g. Neisseria gonorrhoeae or Chlamydia trachomatis) increase the risk of developing ovarian cancer. Bacterial metabolites, produced by the healthy eubiome or the oncobiome, may exert autocrine, paracrine, and hormone-like effects, as was evidenced in breast cancer or pancreas adenocarcinoma. We discuss the possible involvement of lipopolysaccharides, lysophosphatides and tryptophan metabolites, as well as, short-chain fatty acids, secondary bile acids and polyamines in the carcinogenesis of ovarian cancer. We discuss the applicability of nutrients, antibiotics, and probiotics to harness the microbiome and support ovarian cancer therapy. The oncobiome and the most likely bacterial metabolites play vital roles in mediating the effectiveness of chemotherapy. Finally, we discuss the potential of oncobiotic changes as biomarkers for the diagnosis of ovarian cancer and microbial metabolites as possible adjuvant agents in therapy.

Physiological Functions of Bacterial "Multidrug" Efflux Pumps

Bacterial multidrug efflux pumps have come to prominence in human and veterinary pathogenesis because they help bacteria protect themselves against the antimicrobials used to overcome their infections. However, it is increasingly realized that many, probably most, such pumps have physiological roles that are distinct from protection of bacteria against antimicrobials administered by humans. Here we undertake a broad survey of the proteins involved, allied to detailed examples of their evolution, energetics, structures, chemical recognition, and molecular mechanisms, together with the experimental strategies that enable rapid and economical progress in understanding their true physiological roles. Once these roles are established, the knowledge can be harnessed to design more effective drugs, improve existing microbial production of drugs for clinical practice and of feedstocks for commercial exploitation, and even develop more sustainable biological processes that avoid, for example, utilization of petroleum.

Swarming bacteria undergo localized dynamic phase transition to form stress-induced biofilms

Self-organized multicellular behaviors enable cells to adapt and tolerate stressors to a greater degree than isolated cells. However, whether and how cellular communities alter their collective behaviors adaptively upon exposure to stress is largely unclear. Here, we investigate this question using Bacillus subtilis, a model system for bacterial multicellularity. We discover that, upon exposure to a spatial gradient of kanamycin, swarming bacteria activate matrix genes and transit to biofilms. The initial stage of this transition is underpinned by a stress-induced multilayer formation, emerging from a biophysical mechanism reminiscent of motility-induced phase separation (MIPS). The physical nature of the process suggests that stressors which suppress the expansion of swarms would induce biofilm formation. Indeed, a simple physical barrier also induces a swarm-to-biofilm transition. Based on the gained insight, we propose a strategy of antibiotic treatment to inhibit the transition from swarms to biofilms by targeting the localized phase transition.