Name: induction of cellular differentiation and single cell imaging of vibrio parahaemolyticus swimmer and swarmer cells
Uploaded: 2017-05-15T15:00:00.000+00:00
Duration: 8 min 38 s
Description: Watch this Scientific Journal Video about Induction of Cellular Differentiation and Single Cell Imaging of Vibrio parahaemolyticus Swimmer and Swarmer Cells at JoVE.com

This work was supported by the Max Planck Society.

1. Preparation of Electro-competent V. parahaemolyticus Cells and Electroporation of Plasmid DNA into Swimmer Cells
NOTE: The following section of the protocol allows for the preparation of electro-competent cells and the subsequent electroporation of plasmid DNA into swimmer cells. This step is important if fluorescent proteins are being ectopically expressed from a plasmid.
<ol>
	<li>Streak out V. parahaemolyticus cells from a -80 &#176;C glycerol stock onto a fresh LB agar plate containing 100 &#181;g/mL ampicillin and incubate overnight at 37 &#176;C.</li>
	<li>The following day, inoculate 200 mL of LB medium with a single colony of V. parahaemolyticus and incubate it at 37 &#176;C under shaking conditions until an OD600 of 1.0 is reached. It usually takes 5-6 h of incubation for the cell culture to reach the desired optical density.</li>
	<li>Immediately transfer the cells onto ice and perform all further steps on ice and in 4 &#176;C pre-cooled centrifuges.</li>
	<li>Harvest the cells at 4 &#176;C for 10 min at 2,000 x g.</li>
	<li>Discard the supernatant by decantation and re-suspend the cell pellet in 25 mL of ice-cold 273 mM sucrose solution (pH 7.4, buffered with KOH).</li>
	<li>Harvest the cells again at 4 &#176;C for 10 min at 2000 x g. Repeat two additional times.</li>
	<li>Re-suspend the washed cell pellet in 400 &#181;L of ice-cold 273 mM sucrose solution. Subsequently, add glycerol to a final concentration of 15% vol/vol. The cells are now ready for electroporation, but can also be frozen in aliquots of 70 &#181;L at -80 &#176;C for later use.</li>
	<li>For the electroporation, mix a 70 &#181;L aliquot of electro-competent cells with 100 - 1,000 ng of plasmid DNA and transfer the mixture into an ice-cold electroporation cuvette (0.2 cm electrode gap). Perform electroporation with the following settings: 25 &#181;F, 2400 V and 200 &#937;.</li>
	<li>Suspend the cells in the electroporation cuvette in 600 &#181;L of LB broth, transfer to a 2 mL tube and incubate while shaking at 37 &#176;C for 3 h.</li>
	<li>Spin down the cells at 2,000 x g for 5 min and re-suspend the pellet in 100 &#181;L of LB broth. Spread the cell-suspension onto selective LB agar plates containing the necessary antibiotics and incubate at 37 &#176;C overnight.</li>
	<li>The following day, check the plates for colony formation. Colonies that grow carry the correct antibiotic resistance gene encoded on the plasmid and can now be used for further experiments.</li>
</ol>
2. Induction of Swarmer Cell Differentiation
NOTE: The following steps describe how to induce differentiation of V. parahaemolyticus into its swarmer cell life-cycle and how to stimulate proliferation on solid surfaces.
<ol>
	<li>Suspend 4 g of Heart Infusion (HI) Agar in 100 mL ddH2O in order to prepare the swarming plates.</li>
	<li>Carefully boil the HI agar solution in the microwave and shake the bottle from time-to-time until the powder is dissolved. Autoclave at 121 &#176;C for 20 min.</li>
	<li>After autoclaving, cool down the HI agar to 60-65 &#176;C. Add 2,2&#180;-Bipyridyl to a final concentration of 50 &#181;M (stock solution of 50 mM in 100% ethanol). Add CaCl2 to a final concentration of 4 mM (stock solution of 4 M in ddH2O). If necessary, add antibiotics into the solution to maintain plasmids. 
	NOTE: If planning to use an inducible plasmid, add inducing agent to its final concentration. 
	CAUTION: 2,2&#180;-Bipyridyl: Acute toxicity (oral, dermal, inhalation). Use gloves and safety goggles when handling this chemical.</li>
	<li>Pour 30 - 35 mL of the final HI agar solution into a round 150 mm Petri dish and let the agar solidify.</li>
	<li>Right before spotting the cell culture, dry the agar plate at 37 &#176;C for at least 10 min (or until any liquid residues have disappeared, but no longer) up-right with an open lid. 
	NOTE: Drying times highly depend on the incubator used and heavily dried plates will not permit swarming of V. parahaemolyticus. (This step is very important!) Plates must be used fresh and should not be older than 2 - 3 h. Old plates will be too dry to stimulate swarming.</li>
	<li>Inoculate a small amount of cells from the edge of a single colony into 5 mL of LB broth. Incubate the culture shaking at 37 &#176;C until OD600 = 0.8 is reached, it usually takes around 2-3 hours. After that, the cells are ready to be spotted onto HI swarming agar plates.</li>
	<li>Spot 1 &#181;L of cell culture at the center of a HI agar swarming plate (Figure 1A).</li>
	<li>Let the spot dry (Figure 1B).</li>
	<li>Seal the plate with clear plastic tape and make sure that it is firmly attached, otherwise it might detach during overnight incubation (Figure 1C). 
	NOTE: It is very important that the seal is perfect. Avoid the formation of air-bubbles and folds to the tape when it is applied.</li>
	<li>Incubate the plate at 24 &#176;C overnight. This will result in the formation of a V. parahaemolyticus swarm-colony with swarm-flares extending from the periphery of the swarm-colony (Figure 2).</li>
</ol>
3. Preparation of V. parahaemolyticus Swarmer Cells for Fluorescence Microscopy
NOTE: The following protocol describes how to prepare microscopy agarose slides and the subsequent imprinting of swarming flares onto an agarose pad to obtain single swarmer cells for microscopy.
<ol>
	<li>To prepare agarose slides for microscopy, add 1 g of agarose to 100 mL of a 20% vol/vol PBS and 10% vol/vol LB broth solution. Carefully boil the solution in the microwave to dissolve the agarose and let it cool down to 65-70 &#176;C while mixing with a magnetic stirrer.</li>
	<li>Place a clean microscope slide onto a perfectly level section of a working bench. Cover both ends of the slide with two layers of general-purpose laboratory labeling tape, fixing the slide to the working bench. The distance between the two pieces of tape should be around 3 cm. 
	NOTE: The two layers of tape create a very small elevation, which will determine the height of the agarose pad. It is important that the working space is level to make sure cells will be in the same plane for microscopy analysis.</li>
	<li>Pipet ~ 250 &#181;L of the previously prepared agarose solution onto the non-covered glass surface.</li>
	<li>Now place a second microscope slide in the same orientation as the bottom one on-top and slightly press it down, so that residual agarose can flow out to the sides.</li>
	<li>Let the agarose solidify 1-2 min and then slowly pull the top glass slide off the bottom one in a horizontal movement.</li>
	<li>Using a scalpel, cut off any residual agarose that is attached to the sides of the microscope slide and slowly remove the tape from the ends of the microscope slide. 
	NOTE: The agarose slide is now ready and should be used as soon as possible as it will slowly begin to dry out.</li>
	<li>To perform microscopy on swarmer cells, cut out a ~3 mm x 10 mm piece of swarming agar from the most outer edge of a swarming colony (Figure 1D). It is very important not to break the tape seal of the swarm-plate until immediately before transfer of swarmer cells to the microscope slide. Once the tape is removed, swarming V. parahaemolyticus cells initiate differentiation into swimmer cells. 
	NOTE: Make sure to direct the cuts from the outside of the swarming colony edge to the inside of the colony (Figure 1D). This way you can prevent &#34;swimmer contamination&#34; into the edge of the swarming colony.</li>
	<li>Transfer the piece of swarming agar onto a microscope agarose slide with the cells facing the agarose pad (Figure 1E). This imprints the swarming cells onto the agarose pad.</li>
	<li>After waiting ~30 s, remove the agar piece carefully from the agarose pad (Figure 1F).</li>
	<li>Place a glass coverslip onto the agarose pad where the cells were imprinted. The cells are now ready for microscopy. 
	NOTE: It is important to image swarmer cells immediately, since swarmer cells slowly initiate differentiation to the swimmer state.</li>
</ol>
4. Preparation of V. parahaemolyticus Swimmer Cell-cultures For Fluorescence Microscopy
NOTE: This section of the protocol describes how to prepare a culture of V. parahaemolyticus to perform fluorescence microscopy on the swimmer cell-type.
<ol>
	<li>Inoculate a small amount of cells from the edge of a single colony into 5 mL of LB broth. Incubate the culture shaking at 37 &#176;C for 1 h or until slight cell-growth becomes visible.</li>
	<li>At this stage, if needed, add inducing agent for expression of proteins of interest. In this example, L-arabinose was added to a final concentration of 0.2% (w/vol) in order to induce expression of YFP-CheW9.</li>
	<li>Incubate the culture shaking for an additional 2 h at 37 &#176;C.</li>
	<li>Follow steps 3.1-3.7 to prepare microscopy agarose slides.</li>
	<li>Spot 1 &#181;L of cell culture at the center of the agarose pad and let the spot incubate until it is dry.</li>
	<li>Place a glass coverslip onto the agarose pad where the cells were spotted. The cells are now ready to be imaged under the fluorescence microscope.</li>
</ol>
5. Image Analysis
This part of the protocol describes a workflow for image analysis, particularly how to extract fluorescence data of single cells for demographic analysis.
<ol>
	<li>Before beginning the image analysis make sure that all microscopy images are saved in 16bit TIF format.</li>
	<li>Load the DIC (or phase contrast) and the corresponding fluorescent channel images into the software.</li>
	<li>Generate an overlay image of both channels by selecting &#34;Display/Overlay images&#34;. Set the number of pictures (&#34;# Images:&#34;) to two, and select the DIC image in the first channel and the fluorescent image in the second channel.</li>
	<li>Select the &#34;Multi-Line&#34; tool from the toolbar and mark cells from one pole to the other through the middle of the cell. In order to get a list of all generated lines (line objects) open &#34;Measure/Region Measurements&#34;. Configure the region measurements to only display the region label, distance, and average intensity.</li>
	<li>Calibrate the pixel size under &#34;Measure/Calibrate Distances&#34; to the pixel size that is specific for your microscope setup and click &#34;Apply To All Open Images&#34;.</li>
	<li>Transfer all regions (line objects) to the fluorescent channel image. Under &#34;Regions/Transfer Regions&#34; select the source image (the overlay image) and the destination image (the fluorescent channel image). Select &#34;All Regions&#34; and press &#34;OK&#34;. 
	NOTE: To be able to later re-produce the exact lines (line objects, regions, ROI), open &#34;Regions/Save Regions&#34; and save the regions.</li>
	<li>Export all region measurements into a spreadsheet by opening &#34;Measure/Region Measurements&#34; and pressing &#34;Open Log&#34;. Confirm to open and export the data. Once the spreadsheet is opened in the background, finally export the data by pressing &#34;F9: Log Data&#34;.</li>
	<li>To determine the position of fluorescent foci along the cell, open &#34;Measure/Linescan&#34;. Set &#34;Linescan Width&#34; to a value so that the whole width of a cell is covered by the region that you previously created. Right-click into the line-scan graph and select &#34;Show Graph Data&#34;. By left-clicking and dragging the mouse-courser along the line-scan to the point of interest, the &#34;Graph Data&#34; window will display the corresponding pixel/distance between the two points. Select the blue highlighted row and then copy the content. 
	NOTE: The entire line-scan intensity profile can be logged to a spreadsheet by pressing &#34;Log Data&#34; in the &#34;Linescan&#34; window. The extracted data can now be used for visualization in graphs or further statistical analysis. Localization patterns over the cell cycle can be easily visualized in a demographic representation of the cell length and the fluorescent intensities along the cell body. These representations can be obtained using the same ROI&#39;s previously selected. The following steps will give an example of how to generate demographics similar to the ones shown in Figures 3C and 4C.
	<ol>
		<li>In Fiji/ImageJ load region markings (.rgn) previously created in the software (step 5.6) using the &#34;Metamorph nd &#38; ROI files importer&#34;. Alternatively, regions of interest (ROIs) of the cells to be analyzed can be created directly in Fiji/ImageJ using the build-in &#34;Segmented Line&#34; tool.</li>
		<li>Open &#34;Analyze/Tools/ROI manager&#34; and mark all active list entries&#34;.</li>
		<li>Afterward, click &#34;More/Multi Plot&#34; and then select &#34;List&#34; in the new &#34;Multi Plot&#34; window. Click on a table entry, then select and &#34;copy all&#34;. Subsequently, paste into a new spreadsheet. 
		NOTE: Make sure that the data of the longest cell (two corresponding X and Y columns with the most number of rows) is the last one to the right in the spreadsheet.</li>
		<li>Save the spreadsheet as a &#34;CSV (Comma delimited) (*.csv)&#34;.</li>
		<li>Download the R scripts from here &#34;https://github.com/ta-cameron/Cell-Profiles&#8221;10. The scripts sort cells by length and normalize the fluorescent intensity profiles of all cells as an average of each cell&#8217;s fluorescence.</li>
		<li>Run the entire script &#34;cell profiles function.R&#34; in R [version 3.0.1;11].</li>
		<li>Edit the &#34;example plots.R&#34; script in line 30 such that the file path refers to the folder where the previously generated .csv file is saved. Additionally, change the file name &#34;profile.csv&#34; in line 31 to the file name chosen for .csv file generated in step 5.9.4. Afterwards, run &#34;example plots.R&#34; and follow the documentation from &#34;https://github.com/ta-cameron/Cell-Profiles&#8221; as well as the comments from the script file to generate demographic analysis.</li>
	</ol>
	</li>
</ol>

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No conflicts of interest declared.

This paper reports a method for microscopy imaging of V. parahaemolyticus swarmer cells, followed by downstream analyses intended to resolve and quantify the subcellular localization and other features of the studied fluorescently labeled proteins. Although several tools exist for microscopy image processing and analysis14,15,16,17,18, the analysis of...

Bacteria constantly experience changes to their external environment and have developed several techniques to change and adapt their behavior accordingly. One such mechanism involves differentiation into distinct cell types that better complement the altered environment. Differentiation often involves major changes in the regulation of the cell cycle, cell morphology, and the spatiotemporal organization of the cells. One organism that can undergo differentiation is Vibrio parahaemolyticus. V. parahaemolyticus belongs to the Vibrionaceae, whichis a family of proteobacteria that usually inhabit fresh or salt water. Vibrionaceae are widely distributed in the environment and include several species that cause intestinal tract infections in humans, also including Vibrio cholerae.V. parahaemolyticus is a dimorphic organism and is able to differentiate into two distinct cell types as a response to accommodate changes to its external milieu. In aqueous environments, it exists as a short rod-shaped swimmer cell with a single polar flagellum positioned at the old cell pole. Upon surface contact, differentiation into a swarmer cell is triggered. Swarmer cell differentiation involves two major changes: swarmer cell morphogenesis through inhibition of cell division, and the induction of a second flagella system. This results in the formation of a peritrichous and highly elongated rod-shaped swarmer cell, which can either continue the swarmer life-style, where division events results in progeny swarmer cells, or alternatively differentiate back into swimmer cells.
Several factors have been reported to induce or influence swarmer differentiation. The primary stimulus appears to be driven by mechanosensing where V. parahaemolyticus uses the polar flagellum as a tactile sensor that detects inhibition of the rotation upon surface contact, but several other factors are involved as well1. In the lab, rotation of the polar flagellum can be artificially inhibited by addition of phenamil, which blocks the sodium-channel driven flagellar rotation, thereby inducing swarmer differentiation2. Furthermore, in an earlier study, Vibrio alginolyticus was induced to swarm on solid media when cells were propagated on growth medium in a Petri dish sealed with clear plastic tape. Alkali-saturated filter paper prevented swarming under these conditions, hence suggesting that one or more volatile acids might be involved in induction of swarming. Thus, sealing the Petri dish with plastic tape likely allowed for the accumulation of volatile acids, formed as by-products of cellular metabolism, within the head space of the plate. The same effect was achieved when H2O2 was added to the growth medium in un-sealed Petri dishes in order to artificially produce volatile acids by hydrolysing media components3,4,5. Nevertheless, the identity of such volatile acids remains unknown. Moreover, it has been shown that excess availability of calcium6 and iron-limitation7 both enhance swarmer differentiation and proliferation over solid surfaces. Cells can be starved for iron by adding the compound 2,2&#180;-Bipyridyl to the growth medium, which has been shown to influence swarmer differentiation8. The factors known to regulate differentiation are now implemented in the design of a protocol that reproducibly induces V. parahaemolyticus differentiation into swarmer cells and their proliferation on solid agar surfaces.
V. parahaemolyticus differentiation involves major changes in the regulation of cell division, cellular morphology, and the positioning of macromolecular machines such as flagella and chemotaxis apparatuses &#8211; processes that all require the specific localization of proteins in accordance with the cell cycle. Thus, the ability to study the intracellular localization of such proteins is essential to the understanding of the aforementioned cellular processes. In order to perform such studies fluorescence microscopy on single cells is required. This can be particularly challenging when imaging cells that exist within dense bacterial populations, as is the case for swarmer cells. There have been attempts to induce swarmer differentiation in liquid media, which could potentially generate single cells for microscopy studies. And although on a transcriptional level these cells have partially induced the swarmer-differentiation program, they do not undergo the same distinct morphological changes as fully differentiated swarmer cells grown on solid medium8. This paper offers a robust and reproducible protocol of a method to induce swarmer cell differentiation on an agar surface. The protocol produces a population of easily accessible swarmer cells readily available for single cell microscopy and subsequent analysis. Furthermore, the protocol enables localization studies of fluorescently labeled proteins in both the swimmer and swarmer cell-types (sections 1, 2, 3, 4). Additionally, the protocol describes the subsequent workflow on how to process and analyze the generated data from fluorescence microscopy experiments, which allows for demographic analysis of bacterial societies (section 5).

<table><tbody><tr><td>&lt;strong&gt;Media components&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>LB medium</td><td>Roth</td><td>X968.3</td><td></td></tr><tr><td>Difco Agar, granulated</td><td>BD</td><td>214510</td><td>For preparation of LB agar with LB medium</td></tr><tr><td>Difco Heart Infusion Agar</td><td>BD</td><td>244400</td><td>For preparation of HI agar swarming plates</td></tr><tr><td>Agarose NEEO, ultra quality</td><td>Roth</td><td>2267.3</td><td>For preparation of microscopy agarose pads</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Additives&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>L-arabinose</td><td>Roth</td><td>5118.3</td><td>Used to induce pBAD derivatives</td></tr><tr><td>2,2`-Bipyridyl</td><td>Sigma Aldrich</td><td>D216305-25G</td><td>For preparation of HI agar swarming plates</td></tr><tr><td>Calcium chloride dihydrate</td><td>Roth</td><td>5239.1</td><td>For preparation of HI agar swarming plates</td></tr><tr><td>Ampicillin sodium salt</td><td>Roth</td><td>K029.3</td><td></td></tr><tr><td>Chloramphenicol</td><td>Roth</td><td>3886.3</td><td></td></tr><tr><td>PBS buffer</td><td>-</td><td>-</td><td>Standard recipe for Phosphate-buffered saline</td></tr><tr><td>D(+) Sucrose</td><td>Roth</td><td>4621.1</td><td>For preparation of electrocompetent cells</td></tr><tr><td>Glycerol</td><td>Roth</td><td>3783.5</td><td>For preparation of electrocompetent cells</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Hardware&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Petri dish 150 mm x 20 mm with cams</td><td>Sarstedt</td><td>82.1184.500</td><td>For preparation of HI agar swarming plates</td></tr><tr><td>kelvitron t (B 6420)</td><td>Heraeus</td><td>-</td><td>Used for drying HI agar swarming plates</td></tr><tr><td>Gene Pulser Xcell Microbial System</td><td>BioRad</td><td>1652662</td><td>Used for elctroporation of plasmid DNA</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Software&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>MetaMorph Offline (version 7.7.5.0)</td><td>Molecular Devices</td><td>-</td><td>Used for microscopy image analysis</td></tr><tr><td>Excel</td><td>Microsoft</td><td>-</td><td>Used for microscopy data analsis</td></tr></tbody></table>

induction of cellular differentiation and single cell imaging of vibrio parahaemolyticus swimmer and swarmer cells

The ability to study the intracellular localization of proteins is essential for the understanding of many cellular processes. In turn, this requires the ability to obtain single cells for fluorescence microscopy, which can be particularly challenging when imaging cells that exist within bacterial communities. For example, the human pathogen Vibrio parahaemolyticus exists as short rod-shaped swimmer cells in liquid conditions that upon surface contact differentiate into a subpopulation of highly elongated swarmer cells specialized for growth on solid surfaces. This paper presents a method to perform single cell fluorescence microscopy analysis of V. parahaemolyticus in its two differential states. This protocol very reproducibly induces differentiation of V. parahaemolyticus into a swarmer cell life-cycle and facilitates their proliferation over solid surfaces. The method produces flares of differentiated swarmer cells extending from the edge of the swarm-colony. Notably, at the very tip of the swarm-flares, swarmer cells exist in a single layer of cells, which allows for their easy transfer to a microscope slide and subsequent fluorescence microscopy imaging of single cells. Additionally, the workflow of image analysis for demographic representation of bacterial societies is presented. As a proof of principle, the analysis of the intracellular localization of chemotaxis signaling arrays in swimmer and swarmer cells of V. parahaemolyticus is described.

Induction of differentiation and generation of swarming colonies
Figure 1 provides a schema of the important steps involved in producing swarming colonies of V. parahaemolyticus (Figure 1A-C). A swimmer culture was spotted on swarm-agar and incubated at 24 oC, inducing swarmer differentiation and proliferation over the solid agar surface. A representative stereo-microscopy image...

Watch this Scientific Journal Video about Induction of Cellular Differentiation and Single Cell Imaging of Vibrio parahaemolyticus Swimmer and Swarmer Cells at JoVE.com

Induction of Cellular Differentiation and Single Cell Imaging of Vibrio parahaemolyticus Swimmer and Swarmer Cells

This protocol enables single cell microscopy of the differentially distinct Vibrio parahaemolyticus swimmer and swarmer cells. The method produces a population of swarmer cells easily available for single cell analysis and covers preparation of cell cultures, induction of swarmer differentiation, sample preparation, and image analysis.

Induction of Cellular Differentiation and Single Cell Imaging of Vibrio parahaemolyticus Swimmer and Swarmer Cells

The ability to study the intracellular localization of proteins is essential for the understanding of many cellular processes. In turn, this requires the ...

induction-cellular-differentiation-single-cell-imaging-vibrio

Universidad de Cartagena UDEC

Research

JoVE Journal

Immunology and Infection

9.3K Views.  Max Planck Institute for Terrestrial Microbiology. This protocol enables single cell microscopy of the differentially distinct Vibrio parahaemolyticus swimmer and swarmer cells. The method produces a population of swarmer cells easily available for single cell analysis and covers preparation of cell cultures, induction of swarmer differentiation, sample preparation, and image analysis.

Video: Induction of Cellular Differentiation and Single Cell Imaging of Vibrio parahaemolyticus Swimmer and Swarmer Cells

Monitoring Spatial Segregation in Surface Colonizing Microbial Populations

Microbes provide an intriguing system to study social interaction among individuals within a population. The short generation times and relatively simple genetic modification procedures of microbes facilitate the development of the sociomicrobiology field. To assess the fitness of certain microbial species, selected strains or their genetically modified derivatives within one population, can be fluorescently labelled and tracked using microscopy adapted with appropriate fluorescence filters. Expanding colonies of diverse microbial species on agar media can be used to monitor the spatial distribution of cells producing distinctive fluorescent proteins.
Here, we present a detailed protocol for the use of green- and red-fluorescent protein producing bacterial strains to follow spatial arrangement during surface colonization, including flagellum-driven community movement (swarming), exopolysaccharide- and hydrophobin-dependent growth mediated spreading (sliding), and complex colony biofilm formation. Non-domesticated isolates of the Gram-positive bacterium, Bacillus subtilis can be utilized to scrutinize certain surface spreading traits and their effect on two-dimensional distribution on the agar-solidified medium. By altering the number of cells used to initiate colony biofilms, the assortment levels can be varied on a continuous scale. Time-lapse fluorescent microscopy can be used to witness the interaction between different phenotypes and genotypes at a certain assortment level and to determine the relative success of either.

The role of assortment (spatial segregation) in evolutionary scenarios can be examined using simple microbial systems in the laboratory that allow controlled adjustment of spatial distribution. By modifying the founder cell density, various assortment levels can be visualized using fluorescently labelled bacterial strains in the colony biofilms of Bacillus subtilis.

Microbes provide an intriguing system to study social interaction among individuals within a population. The short generation times and relatively simple ...

Genetics

Quantifying Bacterial Surface Swarming Motility on Inducer Gradient Plates

Bacterial swarming motility is a common microbiological phenotype that bacterial communities use to migrate over semisolid surfaces. In investigations of induced swarming motility, specific concentration&#160;of an inducer may not be able to report events occurring within the optimal concentration range to elicit the desired responses from a species. Semisolid plates containing multiple concentrations are commonly used to investigate the response within an inducer concentration range. However, separate semisolid plates increase variations in medium viscosity and moisture content within each plate due to nonuniform solidification time.
This paper describes a one-step method to simultaneously test surface swarming motility on a single gradient plate, where the isometrically arranged test wells allow the simultaneous acquisition of multiconcentration responses. In the present work, the surface swarming of Escherichia coli K12 and Pseudomonas aeruginosa PAO1 were evaluated in response to a concentration gradient of inducers such as resveratrol and arabinose. Periodically, the swarm morphologies were imaged using an imaging system to capture the entire surface swarming process.
The quantitative measurement of the swarm morphologies was acquired using ImageJ software, providing analyzable information of the swarm area. This paper presents a simple gradient swarm plate method that provides qualitative and quantitative information about the inducers&#39; effects on surface swarming, which can be extended to study the effects of other inducers on a broader range of motile bacterial species.

Here, we describe the use of inducer gradient plates to evaluate bacterial swarming motility while simultaneously obtaining multiple concentration responses.

Bacterial swarming motility is a common microbiological phenotype that bacterial communities use to migrate over semisolid surfaces. In investigations of ...

Biochemistry

A Simple Microfluidic Chip for Long-Term Growth and Imaging of Caenorhabditis elegans

Caenorhabditis elegans (C. elegans) have proved to be a valuable model system for studying developmental and cell biological processes. Understanding these biological processes often requires long-term and repeated imaging of the same animal. Long recovery times associated with conventional immobilization methods done on agar pads have detrimental effects on animal health making it inappropriate to repeatedly image the same animal over long periods of time. This paper describes a microfluidic chip design, fabrication method, on-chip C. elegans culturing protocol, and three examples of long-term imaging to study developmental processes in individual animals. The chip, fabricated with polydimethylsiloxane and bonded on a cover glass, immobilizes animals on a glass substrate using an elastomeric membrane that is deflected using nitrogen gas. Complete immobilization of C. elegans enables robust time-lapse imaging of cellular and sub-cellular events in an anesthetic-free manner. A channel geometry with a large cross-section allows the animal to move freely within two partially sealed isolation membranes permitting growth in the channel with a continuous food supply. Using this simple chip, imaging of developmental phenomena such as neuronal process growth, vulval development, and dendritic arborization in the PVD sensory neurons, as the animal grows inside the channel, can be performed. The long-term growth and imaging chip operates with a single pressure line, no external valves, inexpensive fluidic consumables, and utilizes standard worm handling protocols that can easily be adapted by other laboratories using C. elegans.

A Simple Microfluidic Chip for Long-Term Growth and Imaging of Caenorhabditis elegans

The protocol describes a simple microfluidic chip design and microfabrication methodology used to grow C. elegans in presence of a continuous food supply for up to 36 h. The growth and imaging device also enables intermittent long-term high-resolution imaging of cellular and sub-cellular processes during development for several days.

Caenorhabditis elegans (C. elegans) have proved to be a valuable model system for studying developmental and cell biological processes. Understanding ...

Bioengineering

Kinetic Visualization of Single-Cell Interspecies Bacterial Interactions

Polymicrobial communities are ubiquitous in nature, yet studying their interactions at the single-cell level is difficult. Thus, a microscopy-based method has been developed for observing interspecies interactions between two bacterial pathogens. The use of this method to interrogate interactions between a motile Gram-negative pathogen, Pseudomonas aeruginosa and a non-motile Gram-positive pathogen, Staphylococcus aureus is demonstrated here. This protocol consists of co-inoculating each species between a coverslip and an agarose pad, which maintains the cells in a single plane and allows for visualization of bacterial behaviors in both space and time.
Furthermore, the time-lapse microscopy demonstrated here is ideal for visualizing the early interactions that take place between two or more bacterial species, including changes in bacterial species motility in monoculture and in coculture with other species. Due to the nature of the limited sample space in the microscopy setup, this protocol is less applicable for studying later interactions between bacterial species once cell populations are too high. However, there are several different applications of the protocol which include the use of staining for imaging live and dead bacterial cells, quantification of gene or protein expression through fluorescent reporters, and tracking bacterial cell movement in both single species and multispecies experiments.

This live-bacterial cell imaging protocol allows for visualization of interactions between multiple bacterial species at the single-cell level over time. Time-lapse imaging allows for observation of each bacterial species in monoculture or coculture to interrogate interspecies interactions in multispecies bacterial communities, including individual cell motility and viability.

Polymicrobial communities are ubiquitous in nature, yet studying their interactions at the single-cell level is difficult. Thus, a microscopy-based method ...

Automated Analysis of Intracellular Phenotypes of Salmonella Using ImageJ

Salmonella is an enteric pathogen able to invade the intestinal epithelium and replicate in enterocytes, both inside Salmonella-specific vacuoles and free in the cytosol (cytosolic hyper-replication). These different phenotypes of intracellular replication drive to different pathways of pathogenesis, i.e., cytosolic hyper-replication induces inflammatory cell death and extrusion into the gut lumen, while vacuolar replication leads to trans-epithelium penetration and systemic spread. Significant effort was made to create microscopy tools to study the behavior of Salmonella inside invaded cells, such as the pCHAR-Duo fluorescence reporter plasmid that allows discrimination between vacuolar and cytosolic bacteria by differential expression of mCherry and GFP. However, intracellular phenotypes are often manually scored, a time-consuming procedure that limits analysis to a small number of samples and cells. To overcome these limitations, two complementary and automated image analyses were developed using ImageJ, a freely available image analysis software. In the high-throughput protocol, epithelial cells were infected with Salmonella carrying pCHAR-Duo using 96-well plates. Imaging was performed using an automated fluorescence microscope. Then, two image analysis methods were applied to measure the intracellular behavior of Salmonella at different detail levels. The first method measures the overall intracellular bacterial load and the extent of cytosolic hyper-replication. It is fast and allows the scoring of a high number of cells and samples, making it suitable for high-throughput assays such as screening experiments. The second method performs single-cell analysis to determine the percentage of infected cells, the mean vacuolar load of Salmonella, and the cytosolic hyper-replication rate giving greater details about Salmonella behavior inside epithelial cells. The protocols can be performed by specifically designed ImageJ scripts to automatically run batch analyses of the major steps of Salmonella-enterocyte interaction.

Automated Analysis of Intracellular Phenotypes of Salmonella Using ImageJ

Salmonella invades and replicates inside intestinal epithelial cells both in Salmonella-specific vacuoles and free in the cytosol (hyper-replication). A high-throughput fluorescence microscopy-based protocol is described here to quantify the intracellular phenotypes of Salmonella by two complementary image analyses through ImageJ, reaching single-cell resolution and scoring.

Salmonella is an enteric pathogen able to invade the intestinal epithelium and replicate in enterocytes, both inside Salmonella-specific vacuoles and free ...

Preparation, Imaging, and Quantification of Bacterial Surface Motility Assays

Bacterial surface motility, such as swarming, is commonly examined in the laboratory using plate assays that necessitate specific concentrations of agar and sometimes inclusion of specific nutrients in the growth medium. The preparation of such explicit media and surface growth conditions serves to provide the favorable conditions that allow not just bacterial growth but coordinated motility of bacteria over these surfaces within thin liquid films. Reproducibility of swarm plate and other surface motility plate assays can be a major challenge. Especially for more &#8220;temperate swarmers&#8221; that exhibit motility only within agar ranges of 0.4%-0.8% (wt/vol), minor changes in protocol or laboratory environment can greatly influence swarm assay results. &#8220;Wettability&#8221;, or water content at the liquid-solid-air interface of these plate assays, is often a key variable to be controlled. An additional challenge in assessing swarming is how to quantify observed differences between any two (or more) experiments. Here we detail a versatile two-phase protocol to prepare and image swarm assays. We include guidelines to circumvent the challenges commonly associated with swarm assay media preparation and quantification of data from these assays. We specifically demonstrate our method using bacteria that express fluorescent or bioluminescent genetic reporters like green fluorescent protein (GFP), luciferase (lux operon), or cellular stains to enable time-lapse optical imaging. We further demonstrate the ability of our method to track competing swarming species in the same experiment.

Swarming motility is influenced by physical and environmental factors. We describe a two-phase protocol and guidelines to circumvent the challenges commonly associated with swarm assay preparation and data collection. A macroscopic imaging technique is employed to obtain detailed information on swarm behavior that is not provided by current analysis techniques.

Bacterial surface motility, such as swarming, is commonly examined in the laboratory using plate assays that necessitate specific concentrations of agar ...

Biology

Discrimination and Characterization of Heterocellular Populations Using Quantitative Imaging Techniques

Cellular processes are complex and result from the interplay between multiple cell types and their environment. Existing cell biology techniques often do not allow for accurate interpretation of this interplay. Using a quantitative imaging-based approach, we present a high-content protocol for characterizing the dynamic phenotypic responses (i.e. morphology changes, proliferation, apoptosis) of heterogeneous cell populations to changes in environmental stimuli. We highlight our ability to distinguish between cell types based upon either fluorescence intensity or inherent morphology features depending on the application. This platform allows for a more comprehensive characterization of subpopulation response to perturbation while utilizing shorter time, smaller amounts of reagents, and lower likelihood of error than traditional cell biology assays. However, in some cases, cell populations may be difficult to identify and quantitate based on complex cellular features and will require additional troubleshooting; we highlight some of these circumstances in the protocol. We demonstrate this application using response to drug in a cancer model; however, it can easily be applied more broadly to other physiological processes. This protocol allows one to identify subpopulations within a co-culture system and characterize the particular response of each to external stimuli.

We have developed a novel protocol for studying heterocellular population dynamics in response to perturbations. This manuscript describes an imaging-based platform that produces quantitative datasets for simultaneous characterization of multiple cellular phenotypes of heterocellular populations in a robust manner.

Cellular processes are complex and result from the interplay between multiple cell types and their environment. Existing cell biology techniques often do ...

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 &#34;mother machine&#34;-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.

Single-cell Microfluidic Analysis of Bacillus subtilis

We present a method for the microfluidic analysis of individual bacterial cell lineages using Bacillus subtilis as an example. The method overcomes shortcomings of traditional analytical methods in microbiology by allowing observation of hundreds of cell generations under tightly controllable and uniform growth conditions.

Microfluidic technology overcomes many of the limitations to traditional analytical methods in microbiology. Unlike bulk-culture methods, it offers ...

Live-Cell Imaging of the Life Cycle of Bacterial Predator Bdellovibrio bacteriovorus using Time-Lapse Fluorescence Microscopy

Bdellovibrio bacteriovorus is a small gram-negative, obligate predatory bacterium that kills other gram-negative bacteria, including harmful pathogens. Therefore, it is considered a living antibiotic. To apply B. bacteriovorus as a living antibiotic, it is first necessary to understand the major stages of its complex life cycle, particularly its proliferation inside prey. So far, it has been challenging to monitor successive stages of the predatory life cycle in real-time. Presented here is a comprehensive protocol for real-time imaging of the complete life cycle of B. bacteriovorus, especially during its growth inside the host. For this purpose, a system consisting of an agarose pad is used in combination with cell-imaging dishes, in which the predatory cells can move freely beneath the agarose pad while immobilized prey cells are able to form bdelloplasts. The application of a strain producing a fluorescently tagged &#946;-subunit of DNA polymerase III further allows chromosome replication to be monitored during the reproduction phase of the B. bacteriovorus life cycle.

Live-Cell Imaging of the Life Cycle of Bacterial Predator Bdellovibrio bacteriovorus using Time-Lapse Fluorescence Microscopy

Presented here is a protocol that describes monitoring of the complete life cycle of predatory bacterium Bdellovibrio bacteriovorus using time-lapse fluorescence microscopy in combination with an agarose pad and cell-imaging dishes.

Bdellovibrio bacteriovorus is a small gram-negative, obligate predatory bacterium that kills other gram-negative bacteria, including harmful pathogens. ...

Investigating Flagella-Driven Motility in Escherichia coli by Applying Three Established Techniques in a Series

Motility is crucial to the survival and success of many bacterial species. Many methodologies exist to exploit motility to understand signaling pathways, to elucidate the function and assembly of flagellar parts, and to examine and understand patterns of movement. Here we demonstrate a combination of three of these methodologies. Motility in soft agar is the oldest, offering a strong selection for isolating gain-of-function suppressor mutations in motility-impaired strains, where motility is restored through a second mutation. The cell-tethering technique, first employed to demonstrate the rotary nature of the flagellar motor, can be used to assess the impact of signaling effectors on the motor speed and its ability to switch rotational direction. The &#8220;border-crossing&#8221; assay is more recent, where swimming bacteria can be primed to transition into moving collectively as a swarm. In combination, these protocols represent a systematic and powerful approach to identifying components of the motility machinery, and to characterizing their role in different facets of swimming and swarming. They can be easily adapted to study motility in other bacterial species.

Investigating Flagella-Driven Motility in Escherichia coli by Applying Three Established Techniques in a Series

Many bacteria use flagella-driven motility to navigate their environment and colonize favorable surroundings both individually and as a collective. Demonstrated here is the use of three established methods that exploit motility as a selection tool to identify components/pathways contributing to swimming and swarming motility.

Motility is crucial to the survival and success of many bacterial species. Many methodologies exist to exploit motility to understand signaling pathways, ...

Induction of Cellular Differentiation and Single Cell Imaging of Vibrio parahaemolyticus Swimmer and Swarmer Cells

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Monitoring Spatial Segregation in Surface Colonizing Microbial Populations

Quantifying Bacterial Surface Swarming Motility on Inducer Gradient Plates

A Simple Microfluidic Chip for Long-Term Growth and Imaging of Caenorhabditis elegans

Kinetic Visualization of Single-Cell Interspecies Bacterial Interactions

Automated Analysis of Intracellular Phenotypes of Salmonella Using ImageJ

Preparation, Imaging, and Quantification of Bacterial Surface Motility Assays

Discrimination and Characterization of Heterocellular Populations Using Quantitative Imaging Techniques

Single-cell Microfluidic Analysis of Bacillus subtilis

Live-Cell Imaging of the Life Cycle of Bacterial Predator Bdellovibrio bacteriovorus using Time-Lapse Fluorescence Microscopy

Investigating Flagella-Driven Motility in Escherichia coli by Applying Three Established Techniques in a Series