Programmable, Pneumatically Actuated Microfluidic Device with an Integrated Nanochannel Array To Track Development of Individual Bacteria

The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis

During growth, Bacillus subtilis differentiates into subpopulations of motile individuals and non-motile chains, associated with dispersal and biofilm formation, respectively. The two cell types are dictated by the activity of the alternative sigma factor SigD encoded as the penultimate gene of the 27-kb long fla/che flagellar operon. The frequency of SigD-ON motile cells is increased by the heteromeric transcription factor SwrA·DegU that activates the fla/che promoter. Conversely, the frequency of motile cells is decreased by the heteromeric transcription factor SinR·SlrR, but the mechanism and location of inhibition is poorly understood. Here, using ChIP-Seq analysis, we determine the binding sites of the SinR·SlrR heteromer on the genome. We identified two sites within the fla/che operon that were necessary and sufficient to attenuate transcript abundance by causing premature termination upstream of the gene that encodes SigD. Thus, cell motility and the transition to biofilm formation depend on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle. More broadly, our study serves as a model for transcription factors that control transcriptional elongation and the regulation of long operons in bacteria.

The SinR•SlrR heteromer attenuates transcription of a long operon of flagellar genes in Bacillus subtilis

During growth, Bacillus subtilis differentiates into subpopulations of motile individuals and non-motile chains, associated with dispersal and biofilm formation respectively. The two cell types are dictated by the activity of the alternative sigma factor SigD encoded as the penultimate gene of the 27 kb long fla/che flagellar operon. The frequency of SigD-ON motile cells is increased by the heteromeric transcription factor SwrA•DegU that activates the fla/che promoter. Conversely, the frequency of motile cells is decreased by the heteromeric transcription factor SinR•SlrR, but the mechanism and location of inhibition is poorly understood. Here, using ChIP-Seq analysis, we determine the binding sites of the SinR•SlrR heteromer on the genome. We identified two sites within the fla/che operon that were both necessary and sufficient to attenuate transcript abundance by causing premature termination upstream of the gene that encodes SigD. Thus, cell motility and the transition to biofilm formation depend on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle. More broadly, our study serves as a model for transcription factors that control transcriptional elongation and the regulation of long operons in bacteria.

Rapid identification of bacterial isolates using microfluidic adaptive channels and multiplexed fluorescence microscopy

We demonstrate the rapid capture, enrichment, and identification of bacterial pathogens using Adaptive Channel Bacterial Capture (ACBC) devices. Using controlled tuning of device backpressure in polydimethylsiloxane (PDMS) devices, we enable the controlled formation of capture regions capable of trapping bacteria from low cell density samples with near 100% capture efficiency. The technical demands to prepare such devices are much lower compared to conventional methods for bacterial trapping and can be achieved with simple benchtop fabrication methods. We demonstrate the capture and identification of seven species of bacteria with bacterial concentrations lower than 1000 cells per mL, including common Gram-negative and Gram-positive pathogens such as Escherichia coli and Staphylococcus aureus. We further demonstrate that species identification of the trapped bacteria can be undertaken in the order of one-hour using multiplexed 16S rRNA-FISH with identification accuracies of 70-98% with unsupervised classification methods across 7 species of bacteria. Finally, by using the bacterial capture capabilities of the ACBC chip with an ultra-rapid antimicrobial susceptibility testing method employing fluorescence imaging and convolutional neural network (CNN) classification, we demonstrate that we can use the ACBC chip as an imaging flow cytometer that can predict the antibiotic susceptibility of E. coli cells after identification.

The Division Defect of a Bacillus subtilis minD noc Double Mutant Can Be Suppressed by Spx-Dependent and Spx-Independent Mechanisms

During growth, bacteria increase in size and divide. Division is initiated by the formation of the Z-ring, a ring-like cytoskeletal structure formed by treadmilling protofilaments of the tubulin homolog FtsZ. FtsZ localization is thought to be controlled by the Min and Noc systems, and here we explore why cell division fails at high temperature when the Min and Noc systems are simultaneously mutated. Microfluidic analysis of a minD noc double mutant indicated that FtsZ formed proto-Z-rings at periodic interchromosome locations but that the rings failed to mature and become functional. Extragenic suppressor analysis indicated that a variety of mutations restored high temperature growth to the minD noc double mutant, and while many were likely pleiotropic, others implicated the proteolysis of the transcription factor Spx. Further analysis indicated that a Spx-dependent pathway activated the expression of ZapA, a protein that primarily compensates for the absence of Noc. In addition, an Spx-independent pathway reduced the length of the cytokinetic period, perhaps by increasing divisome activity. Finally, we provide evidence of an as-yet-unidentified protein that is activated by Spx and governs the frequency of polar division and minicell formation. IMPORTANCE Bacteria must properly position the location of the cell division machinery in order to grow, divide, and ensure each daughter cell receives one copy of the chromosome. In Bacillus subtilis, cell division site selection depends on the Min and Noc systems, and while neither is individually essential, cells fail to grow at high temperature when both are mutated. Here, we show that cell division fails in the absence of Min and Noc, due not to a defect in FtsZ localization but rather to a failure in the maturation of the cell division machinery. Suppressor mutations that restored growth were selected, and while some activated the expression of ZapA via the Spx stress response pathway, others appeared to directly enhance divisome activity.

Noc Corrals Migration of FtsZ Protofilaments during Cytokinesis in Bacillus subtilis

In bacteria, a condensed structure of FtsZ (Z-ring) recruits cell division machinery at the midcell, and Z-ring formation is discouraged over the chromosome by a poorly understood phenomenon called nucleoid occlusion. In B. subtilis, nucleoid occlusion has been reported to be mediated, at least in part, by the DNA-membrane bridging protein, Noc.

Bacteria that divide by binary fission form FtsZ rings at the geometric midpoint of the cell between the bulk of the replicated nucleoids. In Bacillus subtilis, the DNA- and membrane-binding Noc protein is thought to participate in nucleoid occlusion by preventing FtsZ rings from forming over the chromosome. To explore the role of Noc, we used time-lapse fluorescence microscopy to monitor FtsZ and the nucleoid of cells growing in microfluidic channels. Our data show that Noc does not prevent de novo FtsZ ring formation over the chromosome nor does Noc control cell division site selection. Instead, Noc corrals FtsZ at the cytokinetic ring and reduces migration of protofilaments over the chromosome to the future site of cell division. Moreover, we show that FtsZ protofilaments travel due to a local reduction in ZapA association, and the diffuse FtsZ rings observed in the Noc mutant can be suppressed by ZapA overexpression. Thus, Noc sterically hinders FtsZ migration away from the Z-ring during cytokinesis and retains FtsZ at the postdivisional polar site for full disassembly by the Min system.

The Min System Disassembles FtsZ Foci and Inhibits Polar Peptidoglycan Remodeling in Bacillus subtilis

A microfluidic system coupled with fluorescence microscopy is a powerful approach for quantitative analysis of bacterial growth. Here, we measure parameters of growth and dynamic localization of the cell division initiation protein FtsZ in Bacillus subtilis Consistent with previous reports, we found that after division, FtsZ rings remain at the cell poles, and polar FtsZ ring disassembly coincides with rapid Z-ring accumulation at the midcell. In cells mutated for minD, however, the polar FtsZ rings persist indefinitely, suggesting that the primary function of the Min system is in Z-ring disassembly. The inability to recycle FtsZ monomers in the minD mutant results in the simultaneous maintenance of multiple Z-rings that are restricted by competition for newly synthesized FtsZ. Although the parameters of FtsZ dynamics change in the minD mutant, the overall cell division time remains the same, albeit with elongated cells necessary to accumulate a critical threshold amount of FtsZ for promoting medial division. Finally, the minD mutant characteristically produces minicells composed of polar peptidoglycan shown to be inert for remodeling in the wild type. Polar peptidoglycan, however, loses its inert character in the minD mutant, suggesting that the Min system not only is important for recycling FtsZ but also may have a secondary role in the spatiotemporal regulation of peptidoglycan remodeling.IMPORTANCE Many bacteria grow and divide by binary fission in which a mother cell divides into two identical daughter cells. To produce two equally sized daughters, the division machinery, guided by FtsZ, must dynamically localize to the midcell each cell cycle. Here, we quantitatively analyzed FtsZ dynamics during growth and found that the Min system of Bacillus subtilis is essential to disassemble FtsZ rings after division. Moreover, a failure to efficiently recycle FtsZ results in an increase in cell size. Finally, we show that the Min system has an additional role in inhibiting cell wall turnover and contributes to the "inert" property of cell walls at the poles.

Mixed-scale poly(methyl methacrylate) channel network-based single-particle manipulation via diffusiophoresis

Despite the unique advantages of nanochannels imparted by their small size, their utility is limited by the lack of affordable and versatile fabrication methods. Moreover, nanochannel-incorporated fluidic devices require micro-sized conduit integration for efficient access of liquid samples. In this study, a simple and cost-effective fabrication method for mixed-scale channel networks via hot-embossing of poly(methyl methacrylate) (PMMA) using a carbon stamp is demonstrated. Due to its high rigidity, PMMA ensures collapse-free channel fabrication. The carbon stamp is fabricated using only batch microfabrication and has a convex architecture that allows the fabrication of a complex channel network via a single imprinting process. In addition, the microchannels are connected to nanochannels via three-dimensional (3D) microfunnels that serve as single-particle-entrapment chambers, ensuring smooth transport of samples into the nanochannels. Owing to the 3D geometry of the microfunnels and the small size of the nanochannels, a solute gradient can be generated locally at the microfunnel. This local solute gradient enables the entrapment of microparticles at the microfunnels via diffusiophoresis, which can manipulate the particle motion in a controllable manner, without any external equipment or additional electrode integration into the channels. To the best of our knowledge, this is the first report of diffusiophoresis-based single-particle entrapment.

Colloidal lithography-based fabrication of highly-ordered nanofluidic channels with an ultra-high surface-to-volume ratio

This article shows a new strategy for the fabrication of nanofluidics based on nanoscale gaps in nanopillar arrays. Silicon nanopillar arrays are prepared in a designed position by combining conventional photolithography with colloidal lithography. The nanogaps between the pillars are used as nanochannels for the connection of two polydimethylsiloxane-based microchannels in microfluidics. The gap between neighbouring nanopillars can be accurately controlled by changing the size of initial colloidal spheres and by an etching process, which further determines the dimensions of the nanochannels. At a low ionic strength, the surface charge-governed ion transportation shows that the nanochannels possess the same electrokinetic properties as typical nanofluidics. Benefiting from the advantage of photolithography, large-area nanochannel arrays can be prepared in a parallel manner. Due to the perm-selectivity of the nanochannels, the nanofluidic chips can be used to preconcentrate low concentration samples. The large-area ordered nanostructures preserve their high-throughput property and large surface-to-volume ratio, which shows their great potential in the development of nanofluidics and their applications, such as in the separation of small molecules, energy conversion, etc.

Fluorescence in sub-10 nm channels with an optical enhancement layer

Fluorescence microscopy uniquely enables physical and biological research in micro- and nanofluidic systems. However, in channels with depths below 10 nm, the limited number of fluorophores results in fluorescence intensity below the detection limit of optical microscopes. To overcome this barrier, we applied Fabry-Pérot interference to enhance fluorescence intensity with a silicon nitride layer below the sub-10 nm channel. A silicon nitride layer of suitable thickness can selectively enhance both absorption and emission wavelengths, leading to a fluorescent signal that is enhanced 20-fold and readily imaged with traditional microscopes. To demonstrate this method, we studied the mass transport of a binary solution of ethanol and Rhodamin B in 8 nm nanochannels. The large molecular size of Rhodamin B (∼1.8 nm) relative to the channel depth results in both separation and reduced diffusivity, deviating from behavior at larger scales. This method extends the widely available suite of fluorescence analysis tools and infrastructure to unprecedented sub-10 nm scale with relevance to a wide variety of biomolecular interactions.

Single-cell Microfluidic Analysis of Bacillus subtilis

Microfluidic technology overcomes many of the limitations to traditional analytical methods in microbiology. Unlike bulk-culture methods, it offers single-cell resolution and long observation times spanning hundreds of generations; unlike agarose pad-based microscopy, it has uniform growth conditions that can be tightly controlled. Because the continuous flow of growth medium isolates the cells in a microfluidic device from unpredictable variations in the local chemical environment caused by cell growth and metabolism, authentic changes in gene expression and cell growth in response to specific stimuli can be more confidently observed. Bacillus subtilis is used here as a model bacterial species to demonstrate a "mother machine"-type method for cellular analysis. We show how to construct and plumb a microfluidic device, load it with cells, initiate microscopic imaging, and expose cells to a stimulus by switching from one growth medium to another. A stress-responsive reporter is used as an example to reveal the type of data that may be obtained by this method. We also briefly discuss further applications of this method for other types of experiments, such as analysis of bacterial sporulation.

Role of growth rate on the orientational alignment of Escherichia coli in a slit

We present experimental data on the nematic alignment of Escherichia coli bacteria confined in a slit, with an emphasis on the effect of growth rate and corresponding changes in cell aspect ratio. Global alignment with the channel walls arises from the combination of local nematic ordering of nearby cells, induced by cell division and the elongated shape of the cells, and the preferential orientation of cells proximate to the side walls of the slit. Decreasing the growth rate leads to a decrease in alignment with the walls, which is attributed primarily to effects of changing cell aspect ratio rather than changes in the variance in cell area. Decreasing confinement also reduces the degree of alignment by a similar amount as a decrease in the growth rate, but the distribution of the degree of alignment differs. The onset of alignment with the channel walls is coincident with the slits reaching their steady-state occupancy and connected to the re-orientation of locally aligned regions with respect to the walls during density fluctuations.

High-throughput system-wide engineering and screening for microbial biotechnology

Genetic engineering and screening of large number of cells or populations is a crucial bottleneck in today's systems biology and applied (micro)biology. Instead of using standard methods in bottles, flasks or 96-well plates, scientists are increasingly relying on high-throughput strategies that miniaturize their experiments to the nanoliter and picoliter scale and the single-cell level. In this review, we summarize different high-throughput system-wide genome engineering and screening strategies for microbes. More specifically, we will emphasize the use of multiplex automated genome evolution (MAGE) and CRISPR/Cas systems for high-throughput genome engineering and the application of (lab-on-chip) nanoreactors for high-throughput single-cell or population screening.