Name: coincubation assay for quantifying competitive interactions between vibrio fischeri isolates
Uploaded: 2019-07-22T13:00:00
Description: Watch this Scientific Journal Video about Coincubation Assay for Quantifying Competitive Interactions between Vibrio fischeri Isolates at JoVE.com

We would like to thank reviewers for their helpful feedback. A.N.S. was supported by the Gordon and Betty Moore Foundation through Grant GBMF 255.03 to the Life Sciences Research Foundation.

1. Prepare Strains for Coincubation
<ol>
	<li>Choose an appropriate reference strain that will serve as the target for bacterial competition during the coincubation assay. See Discussion for best practices when selecting a reference strain and how the reference strain will impact results. In this protocol, V. fischeri strain ES114 will serve as the reference strain.</li>
	<li>Determining which selection and screening methods will be used to distinguish between the isolates in coincubat...

<ol>
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D., Blockesh, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacterial+type+VI+secretion+system+facilitates+niche+domination.">Bacterial type VI secretion system facilitates niche domination.</a> Proceedings of the National Academy of Sciences of the United States of America. 115 (36), 8855-8857 (2018).</li><li>Maclntyre, D. L., Miyata, S. T., Kitaoka, M., Pukatzki, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Vibrio+cholerae+type+VI+secretion+system+displays+antimicrobial+properties.">The Vibrio cholerae type VI secretion system displays antimicrobial properties.</a> Proceedings of the National Academy of Sciences of the United States of America. 107 (45), 19520-19524 (2010).</li><li>Salomon, D., Gonzalez, H., Updegraff, B. L., Orth, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vibrio+parahaemolyticus+type+VI+secretion+system+1+is+activated+in+marine+conditions+to+target+bacteria,+and+is+differentially+regulated+from+system+2.">Vibrio parahaemolyticus type VI secretion system 1 is activated in marine conditions to target bacteria, and is differentially regulated from system 2.</a> PloS One. 8 (4), e61086 (2013).</li><li>Sana, T. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Salmonella+Typhimurium+utilizes+a+T6SS-mediated+antibacterial+weapon+to+establish+in+the+host+gut.">Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut.</a> Proceedings of the National Academy of Sciences of the United States of America. 113 (34), E5044-E5051 (2016).</li><li>Schwarz, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Burkholderia+type+VI+secretion+systems+have+distinct+roles+in+eukaryotic+and+bacterial+cell+interactions.">Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions.</a> PLoS Pathogens. 6 (8), e1001068 (2010).</li><li>Wenren, L. M., Sullivan, N. L., Cardarelli, L., Septer, A. N., Gibbs, K. 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A., Kolter, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+developments+in+microbial+interspecies+signaling.">New developments in microbial interspecies signaling.</a> Current Opinion in Microbiology. 12 (2), 205-214 (2009).</li><li>Roelofs, K. G., Coyne, M. J., Gentyala, R. R., Chatzidaki-Livanis, M., Comstock, L. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacteroidales+secreted+antimicrobial+proteins+target+surface+molecules+necessary+for+gut+colonization+and+mediate+competition+in+vivo.">Bacteroidales secreted antimicrobial proteins target surface molecules necessary for gut colonization and mediate competition in vivo.</a> MBio. 7 (4), e01055-e01016 (2016).</li><li>Dey, A., Vassallo, C. N., Conklin, A. C., Pathak, D. 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H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rules+of+engagement:+the+type+VI+secretion+system+in+Vibrio+cholerae.">Rules of engagement: the type VI secretion system in Vibrio cholerae.</a> Trends in microbiology. 25 (4), 267-279 (2017).</li><li>Speare, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacterial+symbionts+use+a+type+VI+secretion+system+to+eliminate+competitors+in+their+natural+host.">Bacterial symbionts use a type VI secretion system to eliminate competitors in their natural host.</a> Proceedings of the National Academy of Sciences of the United States of America. 115 (36), E8528-E8537 (2018).</li><li>Shank, E. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+coculture+to+detect+chemically+mediated+interspecies+interactions.">Using coculture to detect chemically mediated interspecies interactions.</a> Journal of Visualized Experiments. (80), (2013).</li><li>Long, R. A., Rowley, D. C., Zamora, E., Liu, J., Bartlett, D. H., Azam, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Antagonistic+interactions+among+marine+bacteria+impede+the+proliferation+of+Vibrio+cholerae.">Antagonistic interactions among marine bacteria impede the proliferation of Vibrio cholerae.</a> Applied and Environmental Microbiology. 71 (12), 8531-8536 (2005).</li><li>Dunn, A. K., Millikan, D. S., Adin, D. M., Bose, J. L., Stabb, E. 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The coincubation assay described above provides a powerful method to discover interbacterial competition. This approach allowed for the identification of intraspecific competition among V. fischeri isolates and characterization of the competitive mechanism19. Although the method described was optimized for the marine bacterium V. fischeri, it can be easily modified to accommodate other bacterial species including clinical and environmental isolates. It is important to note that c...

This manuscript outlines a culture-based method to determine whether two bacterial isolates are capable of competitive interactions. When studying mixed populations, it is important to assess the extent to which the bacterial isolates interact, particularly whether isolates are directly competing through interference mechanisms. Interference competition refers to interactions where one population directly inhibits the growth or kills a competitor population1. These interactions are important to identify because they can have profound effects on a microbial community&#8217;s structure and function2,3.
Mechanisms for microbial competition have been discovered broadly in genomes of bacteria from diverse environments including both host-associated and free-living bacteria4,5,6,7,8,9. A variety of competition strategies have been described10,11 including diffusible mechanisms, such as bactericidal chemicals1,12 and secreted antimicrobial peptides13, as well as contact-dependent mechanisms that require cell-cell contact to transfer an inhibitory effector into target cells9,14,15,16,17,18.
Although culture-based coincubations are commonly used in microbiology5,8,19, this manuscript outlines how to use the assay to characterize the mechanism of competition, as well as suggestions for adapting the protocol for use with other bacterial species. Furthermore, this method describes multiple approaches for analyzing and presenting the data to answer different questions about the nature of the competitive interactions. Although the techniques described here were used previously to identify the interbacterial killing mechanism underlying intraspecific competition between symbiotic strains of coisolated Vibrio fischeri bacteria19, they are suitable for many bacterial species including environmental isolates and human pathogens, and can be utilized to evaluate both contact-dependent and diffusible competitive mechanisms. Steps in the protocol may require optimization for other bacterial species. Given that more model systems are expanding their studies beyond the use of isogenic organisms to include different genotypes10,16,20,21, this method will be a valuable resource for researchers seeking to understand how competition impacts multi-strain or multi-species systems.

<table>
	<tbody>
		<tr>
			<td>1.5 mL Microcentrifuge Tubes</td>
			<td>Fisher</td>
			<td>05-408-129</td>
			<td></td>
		</tr>
		<tr>
			<td>10 &#956;L multichannel pipette</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>100 &#956;L multichannel pipette</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>300 &#956;L multichannel pipette</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>10 &#956;L single channel pipette</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>20 &#956;L single channel pipette</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>200 &#956;L single channel pipette</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1000 &#956;L single channel pipette</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>24-well plates</td>
			<td>Fisher</td>
			<td>07-200-84</td>
			<td>sterile with lid</td>
		</tr>
		<tr>
			<td>96-well plates</td>
			<td>VWR</td>
			<td>10062-900</td>
			<td>sterile with lid</td>
		</tr>
		<tr>
			<td>Calculator</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Chloramphenicol</td>
			<td>Sigma</td>
			<td>C0378</td>
			<td>stock (20 mg/mL in Ethanol); final concentration in media (2 &#956;g /mL LBS)</td>
		</tr>
		<tr>
			<td>Fluorescence dissecting microscope with camera and imaging software</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>forceps</td>
			<td>Fisher</td>
			<td>08-880</td>
			<td></td>
		</tr>
		<tr>
			<td>Kanamycin Sulfate</td>
			<td>Fisher</td>
			<td>BP906-5</td>
			<td>stock (100 mg/mL in water, filter sterilize); final concentration in media (1 &#956;g/mL LBS)</td>
		</tr>
		<tr>
			<td>Nitrocellulose membrane (FS MCE, 25MM, NS)</td>
			<td>Fisher</td>
			<td>SA1J788H5</td>
			<td>0.22 &#956;m nitrocellulose membrane (pk of 100)</td>
		</tr>
		<tr>
			<td>petri plates</td>
			<td>Fisher</td>
			<td>FB0875713</td>
			<td>sterile with lid</td>
		</tr>
		<tr>
			<td>Spectrophotometer</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Semi-micro cuvettes</td>
			<td>VWR</td>
			<td>97000-586</td>
			<td></td>
		</tr>
		<tr>
			<td>TipOne 0.1-10 &#956;L starter system</td>
			<td>USA Scientific</td>
			<td>1111-3500</td>
			<td>10 racks</td>
		</tr>
		<tr>
			<td>TipOne 200 &#956;L starter system</td>
			<td>USA Scientific</td>
			<td>1111-500</td>
			<td>10 racks</td>
		</tr>
		<tr>
			<td>TipOne 1000 &#956;L starter system</td>
			<td>USA Scientific</td>
			<td>1111-2520</td>
			<td>10 racks</td>
		</tr>
		<tr>
			<td>Vortex</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>LBS media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1M Tris Buffer (pH ~7.5)</td>
			<td></td>
			<td></td>
			<td>50 mL 1 M stock buffer (62 mL HCl, 938 mL DI water, 121 g Trizma Base)</td>
		</tr>
		<tr>
			<td>Agar Technical</td>
			<td>Fisher</td>
			<td>DF0812-17-9</td>
			<td>15 g (Add only for plates)</td>
		</tr>
		<tr>
			<td>DI water</td>
			<td></td>
			<td></td>
			<td>950 mL</td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>Fisher</td>
			<td>S640-3</td>
			<td>20 g</td>
		</tr>
		<tr>
			<td>Tryptone</td>
			<td>Fisher</td>
			<td>BP97265</td>
			<td>10 g</td>
		</tr>
		<tr>
			<td>Yeast Extract</td>
			<td>Fisher</td>
			<td>BP9727-2</td>
			<td>5 g</td>
		</tr>
	</tbody>
</table>

coincubation assay for quantifying competitive interactions between vibrio fischeri isolates

This manuscript describes a culture-based, coincubation assay for detecting and characterizing competitive interactions between two bacterial populations. This method employs stable plasmids that allow each population to be differentially tagged with distinct antibiotic resistance capabilities and fluorescent proteins for selection and visual discrimination of each population, respectively. Here, we describe the preparation and coincubation of competing Vibrio fischeri strains, fluorescence microscopy imaging, and quantitative data analysis. This approach is simple, yields quick results, and can be used to determine whether one population kills or inhibits the growth of another population, and whether competition is mediated through a diffusible molecule or requires direct cell-cell contact. Because each bacterial population expresses a different fluorescent protein, the assay permits the spatial discrimination of competing populations within a mixed colony. Although the described methods are performed with the symbiotic bacterium V. fischeri using conditions optimized for this species, the protocol can be adapted for most culturable bacterial isolates.

In order to assess competitive interactions between bacterial populations, a coincubation assay protocol was developed and optimized for V. fischeri. This method utilizes stable plasmids that encode antibiotic resistance genes and fluorescent proteins, allowing for differential selection and visual discrimination of each strain. By analyzing the data collected from the coincubation assay, the competitive outcome of an interaction and the mechanism of the interaction can be identi...

Watch this Scientific Journal Video about Coincubation Assay for Quantifying Competitive Interactions between Vibrio fischeri Isolates at JoVE.com

Coincubation Assay for Quantifying Competitive Interactions between Vibrio fischeri Isolates

Bacteria encode diverse mechanisms for engaging in interbacterial competition. Here, we present a culture-based protocol for characterizing competitive interactions between bacterial isolates and how they impact the spatial structure of a mixed population.

Coincubation Assay for Quantifying Competitive Interactions between Vibrio fischeri Isolates

This manuscript describes a culture-based, coincubation assay for detecting and characterizing competitive interactions between two bacterial populations. ...

Our protocol provides a simple yet robust approach to identify and characterize competitive mechanisms between different strains of Vibrio fischeri bacteria. This method uses stable plasmids that encode different antibiotic resistance genes and fluorescent proteins that allow for differential selection and visual discrimination of each bacterial strain in a mixed culture. To begin, use a sterile toothpick to scrape the cells from the agar plate in the size of a grain of rice.Resuspend the cells in a 1.5 milliliter microcentrifuge tube containing one milliliter of LBS broth. To break up the cell clumps, press them into the side of the tube and then pipette up and down vigorously. Close the tube and vortex for one to two seconds and repeat if the cell clumps are still visible until the sample is visually uniform.Repeat these preparation steps from cell scraping to vortexing for all samples. Measure and record the optical density at 600 nanometers for all samples. To obtain an accurate OD measurement, dilute the samples up to 10-fold using LBS broth.Then normalize each sample to the desired OD 600. To mix the reference strain and competitor strain in a one to one ratio, add 100 microliters of each strain normalized to OD 1.0 to a labeled 1.5 milliliter centrifuge tube and vortex for one to two seconds. As a control, mix the reference strain with a differentially tagged version of itself and vortex as well.It is critical to achieve the correct starting ratio as it can considerably change the outcome of the experiment. To ensure success, this step may require optimization for a given bacterial species. After repeating this step for each biological replicate, there should be four biological replicates with differentially tagged reference strains as controls and four biological replicates with differentially tagged reference and competitor strains.To make culture spots that will be used for fluorescence microscopy after the incubation, add 10 microliters of each control and experimental mixture onto a Petri plate containing LBS agar. After the spots have completely dried on the bench, incubate the plates at 24 degrees Celsius for 24 hours. To make culture spots that will be used to quantify the colony forming units for each strain at the end of the experiment, add 10 microliters of each control and experimental mixtures into 24 well plates containing one milliliter of LBS agar per well.After the spots have completely dried, incubate the plates at 24 degrees Celsius for five hours. To perform a serial dilution of starting coincubation mixtures, rotate a 96 well plate 90 degrees so there are eight columns and 12 rows. Label each row with the strain ID, the replicate number, and the time starting with t zero.Label the LBS agar plates supplemented with the appropriate antibiotic on which to spot the dilution series while making sure to identify which strain each antibiotic plate is selecting for. With a multi-channel pipette, add 180 microliters of LBS broth to each well leaving the first column empty for the undiluted coincubation mixture. Using a 200 microliter single channel pipette, transfer 100 microliters of the coincubation mixture from the tube to the first well of the first column, then discard the tip and repeat for all coincubation mixtures.With a multi-channel pipette, transfer 20 microliters from column one to column two and pipette up and down to mix. Discard the tips and repeat for each column while being consistent with the number of pipetting up and down for each dilution. By the end, each row will contain a 10-fold serial dilution of the initial mixture.Use a multi-channel pipette fitted with eight tips to aspirate five microliters from each well in a dilution series and spot onto the Kanamycin supplemented LBS agar plate that selects for the reference strain. Repeat this step to select for the competitor strain spotting onto the Chloramphenicol supplemented plate. After the spots have dried completely, place the plates in the incubator at 24 degrees Celsius.After the coincubation spots and the 24 well plates have been incubated for five hours at 24 degrees Celsius, add one milliliter of LBS broth to each well. Resuspend by pipetting up and down until all cells have been resuspended being consistent with the vigor in which the cells are resuspended across all replicates. Once each coincubation spot is resuspended, prepare a 96 well plate for a serial dilution and LBS agar plates with the appropriate antibiotics on which to spot the dilution in the same way as previously done.To complete the serial dilution for t final measurements in the 24 well plates, perform steps used for the serial dilution of the starting inoculum and spot each dilution on LBS agar plates as done previously. Proceed with imaging the coincubation spots on the Petri plates and data analysis as described in the manuscript. In the experimental treatment, the reference strain and competitor strain one are present at a proportion of 0.5 at the beginning and end of the experiment consistent with the control treatment.Log RCI values were not statistically different from zero for the control treatment or when the reference strain was incubated with competitor strain one. These data suggest that there was no competition between the reference strain and competitor strain one. By contrast, when the reference strain was incubated with competitor strain two, the reference strain decreased from a proportion of 0.5 at the beginning to a proportion less than 0.01 at the end of the experiment.Furthermore, log RCI values were significantly greater than zero when the reference strain was incubated with competitor strain two. Together, these data indicate that the proportion of the reference strain decreased in the presence of competitor strain two suggesting competition between the strains. When the reference strain was incubated with competitor strain one, CFUs of both strains increased over the course of five hours and were not significantly different suggesting that no competition occurred.Also, approximately 3200%recovery was observed which was not statistically different from the control. However, when the reference strain was incubated with competitor strain two, reference strain CFUs were significantly lower than strain two CFUs in the control at five hours. Also, approximately 4%recovery was observed significantly lower than the control.Altogether, these data indicate that strain two out competed the reference strain by killing its cells. The most important step in this procedure is achieving the correct starting ratio as it can significantly impact results.

Research

JoVE Journal

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