Adaptive Evolution of Escherichia coli to Ciprofloxacin in Controlled Stress Environments: Contrasting Patterns of Resistance in Spatially Varying versus Uniformly Mixed Concentration Conditions

Altered Cell Viability, Morphology, and Motility under Ciprofloxacin Stress Influence the Transport and Resistance of Bacteria in Saturated Porous Media

The ubiquitous occurrence of antibiotics in the environment induces various stress responses of microbes and increases the risk of the emergence and spread of antimicrobial resistance (AMR). In this study, the transport and retention of Shewanella oneidensis cells in saturated porous media was investigated under different levels of ciprofloxacin (CIP) stress. Exposing to lethal CIP stress caused significant viability loss and stimulated cell transport due to increasing hydrophilicity and decreasing surface roughness. While exposure to sublethal CIP stress did not affect MR-1's viability, elongation of cells promoted their retention in sand columns via straining and orientation effects. The elongated cells likely adopted an end-on configuration to minimize repulsive interaction energy when approaching sand surfaces and deposited in a side-on position due to local surface roughness and charge heterogeneity of sands. The more diminished breakthrough of MR-1 cells in redox-active media was ascribed to their improving extracellular electron transfer and energy taxis activities under sublethal CIP stress. Moreover, the retention of elongated cells in porous media facilitated the de novo emergence of a resistant gyrase mutant, whose remobilization might exacerbate the AMR dissemination.

Modeling the Migration and Growth of Shewanella Oneidensis MR-1 in a Diffusion-Dominated Microfluidic Gradient Chamber Under the Influence of an Antibiotic Concentration Gradient

Motility and chemotaxis allow bacteria to migrate from areas that become depleted in energy yielding substrates to more favorable locations, possibly enhancing the biodegradation of pollutants in soil and groundwater. However, in some cases substrates are co-mingled with one or more toxic solutes that inhibit pollutant degradation and/or microbial growth, and the impacts on motility and chemotaxis represent a knowledge gap. In this study, a one-dimensional diffusion reaction model is developed and used to simulate dissimilatory biological reduction of nitrate to ammonia (DNRA) presented in a previously published microfluidic gradient chamber (MGC) experiment, where spatial abundances of Shewanella oneidensis MR-1 cells were recorded over 5 days in a diffusion limited porous media domain as it degraded nitrate and lactate introduced from opposite boundaries, and at one boundary co-mixed with the antibiotic ciprofloxacin. The model considers S. oneidensis chemotaxis toward nitrate and nitrite, random motility, and growth inhibition by ciprofloxacin. Parameters were adjusted within ranges commonly reported in the literature to obtain results that agreed with the data. Simulation results indicate that motility and not chemotaxis, in combination with inhibition of cell growth by ciprofloxacin, controls the distribution of cells in the toxic region (containing ciprofloxacin) of the MGC. This suggests that cell motility may facilitate nitrate removal in soil and groundwater by enabling microorganisms to migrate toward nitrate contaminated regions with elevated antibiotic concentrations.

Deciphering population-level response under spatial drug heterogeneity on microhabitat structures

Bacteria and cancer cells live in a spatially heterogeneous environment, where migration shapes the microhabitat structures critical for colonization and metastasis. The interplay between growth, migration, and microhabitat structure complicates the prediction of population responses to drugs, such as clearance or sustained growth, posing a longstanding challenge. Here, we disentangle growth-migration dynamics and identify that population decline is determined by two decoupled terms: a spatial growth variation term and a microhabitat structure term. Notably, the microhabitat structure term can be interpreted as a dynamic-related centrality measure. For fixed spatial drug arrangements, we show that interpreting these centralities reveals how different network structures, even with identical edge densities, microhabitat numbers, and spatial heterogeneity, can lead to distinct population-level responses. Increasing edge density shifts the population response from growth to clearance, supporting an inversed centrality-connectivity relationship, and mirroring the effects of higher migration rates. Furthermore, we derive a sufficient condition for robust population decline across various spatial growth rate arrangements, regardless of spatial-temporal fluctuations induced by drugs. Additionally, we demonstrate that varying the maximum growth-to-death ratio, determined by drug-bacteria interactions, can lead to distinct population decline profiles and a minimal decline phase emerges. These findings address key challenges in predicting population-level responses and provide insights into divergent clinical outcomes under identical drug dosages. This work may offer a new method of interpreting treatment dynamics and potential approaches for optimizing spatially explicit drug dosing strategies.

Linking spatial drug heterogeneity to microbial growth dynamics in theory and experiment

Diffusion and migration play pivotal roles in microbial communities - shaping, for example, colonization in new environments and the maintenance of spatial structures of biodiversity. While previous research has extensively studied free diffusion, such as range expansion, there remains a gap in understanding the effects of biologically or physically deleterious confined environments. In this study, we examine the interplay between migration and spatial drug heterogeneity within an experimental meta-community of E. faecalis, a Gram-positive opportunistic pathogen. When the community is confined to spatially-extended habitats ('islands') bordered by deleterious conditions, we find that the population level response depends on the trade-off between the growth rate within the island and the rate of transfer into regions with harsher conditions, a phenomenon we explore by modulating antibiotic concentration within the island. In heterogeneous islands, composed of spatially patterned patches that support varying levels of growth, the population's fate depends critically on the specific spatial arrangement of these patches - the same spatially averaged growth rate leads to diverging responses. These results are qualitatively captured by simple simulations, and analytical expressions which we derive using first-order perturbation approximations to reaction-diffusion models with explicit spatial dependence. Among all possible spatial arrangements, our theoretical and experimental findings reveal that the arrangement with the highest growth rates at the center most effectively mitigates population decline, while the arrangement with the lowest growth rates at the center is the least effective. Extending this approach to more complex experimental communities with varied spatial structures, such as a ring-structured community, further validates the impact of spatial drug arrangement. Our findings suggest new approaches to interpreting diverging clinical outcomes when applying identical drug doses and inform the possible optimization of spatially-explicit dosing strategies.

Adaptive Laboratory Evolution of Probiotics toward Oxidative Stress Using a Microfluidic-Based Platform

Adaptive laboratory evolution (ALE) can be used to make bacteria less susceptible to oxidative stress. An alternative to large batch scale ALE cultures is to use microfluidic platforms, which are often more economical and more efficient. Microfluidic ALE platforms have shown promise, but many have suffered from subpar cell passaging mechanisms and poor spatial definition. A new approach is presented using a microfluidic Evolution on a Chip (EVoc) design which progressively drives microbial cells from areas of lower H2O2 concentration to areas of higher concentration. Prolonged exposure, up to 72 h, revealed the survival of adaptive strains of Lacticaseibacillus rhamnosus GG, a beneficial probiotic often included in food products. After performing ALE on this microfluidic platform, the bacteria persisted under high H2O2 concentrations in repeated trials. After two progressive exposures, the ability of L. rhamnosus to grow in the presence of H2O2 increased from 1 mm H2O2 after a lag time of 31 h to 1 mm after 21 h, 2 mm after 28 h, and 3 mm after 42 h. The adaptive strains have different morphology, and gene expression compared to wild type, and genome sequencing revealed a potentially meaningful single nucleotide mutation in the protein omega-amidase.

Microfluidics for adaptation of microorganisms to stress: design and application

Microfluidic systems have fundamentally transformed the realm of adaptive laboratory evolution (ALE) for microorganisms by offering unparalleled control over environmental conditions, thereby optimizing mutant generation and desired trait selection. This review summarizes the substantial influence of microfluidic technologies and their design paradigms on microbial adaptation, with a primary focus on leveraging spatial stressor concentration gradients to enhance microbial growth in challenging environments. Specifically, microfluidic platforms tailored for scaled-down ALE processes not only enable highly autonomous and precise setups but also incorporate novel functionalities. These capabilities encompass fostering the growth of biofilms alongside planktonic cells, refining selection gradient profiles, and simulating adaptation dynamics akin to natural habitats. The integration of these aspects enables shaping phenotypes under pressure, presenting an unprecedented avenue for developing robust, stress-resistant strains, a feat not easily attainable using conventional ALE setups. The versatility of these microfluidic systems is not limited to fundamental research but also offers promising applications in various areas of stress resistance. As microfluidic technologies continue to evolve and merge with cutting-edge methodologies, they possess the potential not only to redefine the landscape of microbial adaptation studies but also to expedite advancements in various biotechnological areas. KEY POINTS: • Microfluidics enable precise microbial adaptation in controlled gradients. • Microfluidic ALE offers insights into stress resistance and distinguishes between resistance and persistence. • Integration of adaptation-influencing factors in microfluidic setups facilitates efficient generation of stress-resistant strains.

Maintaining Antibacterial Activity against Biofouling Using a Quaternary Ammonium Membrane Coupling with Electrorepulsion

Antibacterial modification is a chemical-free method to mitigate biofouling, but surface accumulation of bacteria shields antibacterial groups and presents a significant challenge in persistently preventing membrane biofouling. Herein, a great synergistic effect of electrorepulsion and quaternary ammonium (QA) inactivation on maintaining antibacterial activity against biofouling has been investigated using an electrically conductive QA membrane (eQAM), which was fabricated by polymerization of pyrrole with QA compounds. The electrokinetic force between negatively charged Escherichia coli and cathodic eQAM prevented E. coli cells from reaching the membrane surface. More importantly, cathodic eQAM accelerated the detachment of cells from the eQAM surface, particularly for dead cells whose adhesion capacity was impaired by inactivation. The number of dead cells on the eQAM surface was declined by 81.2% while the number of live cells only decreased by 49.9%. Characterization of bacteria accumulation onto the membrane surface using an electrochemical quartz crystal microbalance revealed that the electrorepulsion accounted for the cell detachment rather than inactivation. In addition, QA inactivation mainly contributed to minimizing the cell adhesion capacity. Consequently, the membrane fouling was significantly declined, and the final normalized water flux was promoted higher than 20% with the synergistic effect of electrorepulsion and QA inactivation. This work provides a unique long-lasting strategy to mitigate membrane biofouling.

Emergence of Resistant Escherichia coli Mutants in Microfluidic On-Chip Antibiotic Gradients

Spatiotemporal structures and heterogeneities are common in natural habitats, yet their role in the evolution of antibiotic resistance is still to be uncovered. We applied a microfluidic gradient generator device to study the emergence of resistant bacteria in spatial ciprofloxacin gradients. We observed biofilm formation in regions with sub-inhibitory concentrations of antibiotics, which quickly expanded into the high antibiotic regions. In the absence of an explicit structure of the habitat, this multicellular formation led to a spatial structure of the population with local competition and limited migration. Therefore, such structures can function as amplifiers of selection and aid the spread of beneficial mutations. We found that the physical environment itself induces stress-related mutations that later prove beneficial when cells are exposed to antibiotics. This shift in function suggests that exaptation occurs in such experimental scenarios. The above two processes pave the way for the subsequent emergence of highly resistant specific mutations.

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.

The role of chemotaxis and efflux pumps on nitrate reduction in the toxic regions of a ciprofloxacin concentration gradient

Spatial concentration gradients of antibiotics are prevalent in the natural environment. Yet, the microbial response in these heterogeneous systems remains poorly understood. We used a microfluidic reactor to create an artificial microscopic ecosystem that generates diffusive gradients of solutes across interconnected microenvironments. With this reactor, we showed that chemotaxis toward a soluble electron acceptor (nitrate) allowed Shewanella oneidensis MR-1 to inhabit and sustain metabolic activity in highly toxic regions of the antibiotic ciprofloxacin (>80× minimum inhibitory concentration, MIC). Acquired antibiotic resistance was not observed for cells extracted from the reactor, so we explored the role of transient adaptive resistance by probing multidrug resistance (MDR) efflux pumps, ancient elements that are important for bacterial physiology and virulence. Accordingly, we constructed an efflux pump deficient mutant (∆mexF) and used resistance-nodulation-division (RND) efflux pump inhibitors (EPIs). While batch results showed the importance of RND efflux pumps for microbial survival, microfluidic studies indicated that these pumps were not necessary for survival in antibiotic gradients. Our work contributes to an emerging body of knowledge deciphering the effects of antibiotic spatial heterogeneity on microorganisms and highlights differences of microbial response in these systems versus well-mixed batch conditions.

Impact of antibiotic concentration gradients on nitrate reduction and antibiotic resistance in a microfluidic gradient chamber

In order to explore the impact of antibiotics on the bacterial metabolic cycling of nitrate within contaminated soil and groundwater environments, we compared the effects of polymyxin B (PMB) and ciprofloxacin (CIP) concentration gradients on the distribution and activity of a wild type (WT) and a flagella deficient mutant (Δflag) of Shewanella oneidensis MR-1 in a microfluidic gradient chamber (MGC). Complementary batch experiments were performed to measure bacteriostatic versus bactericidal concentrations of the two antibiotics, as well as their effect on nitrate reduction. Prior work demonstrated that PMB disrupts cell membranes while CIP inhibits DNA synthesis. Consistent with these modes of action, batch results from this work show that PMB is bactericidal at lower concentrations than CIP relative to their respective minimum inhibitory concentrations (MICs) (≥5× MIC_PMB vs. ≥20× MIC_CIP). Concentration gradients from 0 to 50× the MIC of both antibiotics were established in the MGC across a 2-cm interconnected pore network, with nutrients injected at both concentration boundaries. The WT cells could only access and reduce nitrate in regions of the MGC with PMB at <18× MIC_PMB, whereas this occurred with CIP up to 50× MIC_CIP; and cells extracted from these MGCs showed no antibiotic resistance. The distribution of Δflag cells was further limited to lower antibiotic concentrations (≤1× MIC_PMB, ≤43× MIC_CIP) due to inability of movement. These results indicate that S. oneidensis access and reduce nitrate in bactericidal regions via chemotactic migration without development of antibiotic resistance, and that this migration is inhibited by acutely lethal bactericidal levels of antibiotics.

Human kidney stones: a natural record of universal biomineralization

GeoBioMed - a new transdisciplinary approach that integrates the fields of geology, biology and medicine - reveals that kidney stones composed of calcium-rich minerals precipitate from a continuum of repeated events of crystallization, dissolution and recrystallization that result from the same fundamental natural processes that have governed billions of years of biomineralization on Earth. This contextual change in our understanding of renal stone formation opens fundamentally new avenues of human kidney stone investigation that include analyses of crystalline structure and stratigraphy, diagenetic phase transitions, and paragenetic sequences across broad length scales from hundreds of nanometres to centimetres (five Powers of 10). This paradigm shift has also enabled the development of a new kidney stone classification scheme according to thermodynamic energetics and crystalline architecture. Evidence suggests that ≥50% of the total volume of individual stones have undergone repeated in vivo dissolution and recrystallization. Amorphous calcium phosphate and hydroxyapatite spherules coalesce to form planar concentric zoning and sector zones that indicate disequilibrium precipitation. In addition, calcium oxalate dihydrate and calcium oxalate monohydrate crystal aggregates exhibit high-frequency organic-matter-rich and mineral-rich nanolayering that is orders of magnitude higher than layering observed in analogous coral reef, Roman aqueduct, cave, deep subsurface and hot-spring deposits. This higher frequency nanolayering represents the unique microenvironment of the kidney in which potent crystallization promoters and inhibitors are working in opposition. These GeoBioMed insights identify previously unexplored strategies for development and testing of new clinical therapies for the prevention and treatment of kidney stones.

Microbial community response to ciprofloxacin toxicity in sponge membrane bioreactor

This study aims to offer insights into how ciprofloxacin (CIP) impact bacterial community structures in the Sponge-MBR process when CIP is spiked into hospital wastewater. We found that the CIP toxicity decreased richness critical phylotypes such as phylum class ẟ-, β-, ɣ-proteobacteria, and Flavobacteria that co-respond to suppress denitrification and cake fouling to 37% and 28% respectively. Cluster analysis shows that the different community structures were formed under the influence of CIP toxicity. CIP decreased attached growth biomass by 2.3 times while increasing the concentration of permeate nitrate by 3.8 times, greatly affecting TN removal by up to 26%. Ammonia removal was kept stable by inflating the ammonia removal rate (p < 0.003), with the wealthy Nitrospira genus guaranteeing the nitrification activity. In addition, we observed an increasing richness of Chloroflexi and Planctomycetes, which may play a role in fouling reduction in the Sponge-MBR. Therefore, if the amount of antibiotics in hospital wastewater continues to increase, it is so important to extend biomass retention for denitrification recovery.

Microfluidic Evolution-On-A-Chip Reveals New Mutations that Cause Antibiotic Resistance

Microfluidic devices can mimic naturally occurring microenvironments and create microbial population heterogeneities ranging from planktonic cells to biofilm states. The exposure of such populations to spatially organized stress gradients can promote their adaptation into complex phenotypes, which are otherwise difficult to achieve with conventional experimental setups. Here a microfluidic chip that employs precise chemical gradients in consecutive microcompartments to perform microbial adaptive laboratory evolution (ALE), a key tool to study evolution in fundamental and applied contexts is described. In the chip developed here, microbial cells can be exposed to a defined profile of stressors such as antibiotics. By modulating this profile, stress adaptation in the chip through resistance or persistence can be specifically controlled. Importantly, chip-based ALE leads to the discovery of previously unknown mutations in Escherichia coli that confer resistance to nalidixic acid. The microfluidic device presented here can enhance the occurrence of mutations employing defined micro-environmental conditions to generate data to better understand the parameters that influence the mechanisms of antibiotic resistance.

The role of morphological changes in algae adaptation to nutrient stress at the single-cell level

Individual cell heterogeneity within a population can be critical to its peculiar function and fate. Conventional algal cell-based assays mainly analyze the average responses from a population of algal cells. Therefore, the mechanisms through which changes in population characteristics are driven by the behavior of single algal cells are still not well understood. Algal cells may modulate their physiology and metabolism by changing their morphology in response to environmental stress. In this study, an algal single-cell culture and analysis system was developed to investigate the potential role of morphological changes by algal cells during adaptation to nutrient stress based on a microwell array chip. The surface-to-volume ratio of Microcystis aeruginosa (M. aeruginosa) and the volume of Scenedesmus obliquus (S. obliquus) significantly increased with increasing culture time under nutrient stress. The eccentricity of M. aeruginosa and S. obliquus gradually increased and decreased, respectively, with increasing culture time, indicating that the morphology of M. aeruginosa and S. obliquus became increasingly irregular and regular, respectively, under nutrient stress. There were significant correlations between the morphological characteristics and physiological characteristics of M. aeruginosa and S. obliquus under nutrient stress. In M. aeruginosa, an increased surface-to-volume ratio facilitated a high specific fluorescence intensity, specific Raman intensity, and maximum electron transport rate. In S. obliquus, increased cell volume enhanced nutrient absorption, which facilitated a higher specific growth rate. M. aeruginosa and S. obliquus adopted different adaptation strategies in response to nutrient stress based on morphological changes. These findings facilitate the development of management strategies for controlling harmful cyanobacterial blooms.