Name: using coculture to detect chemically mediated interspecies interactions
Uploaded: 2013-10-31T19:30:00
Description: Watch this Scientific Journal Video about Using Coculture to Detect Chemically Mediated Interspecies Interactions at JoVE.com

The author thanks Roberto Kolter (Harvard Medical School) for his invaluable advice and assistance during the development of this coculture screen. She also thanks Matthew Powers for reading the manuscript for clarity, and Chia-yi Cheng for assistance with obtaining Figure 6.

1. Select a Reporter Gene and Construct a Fluorescent Transcriptional Reporter
For B. subtilis:
<ol>
	<li>See the JoVE article in reference 19 for a protocol describing the construction of fluorescent transcriptional reporters in Bacillus subtilis.</li>
</ol>
For other bacterial species:
<ol>
	<li>Identify a gene that is upregulated during the physiological response of interest. This can be based on existing literature or tran...

<ol>
	<li>Berdy, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bioactive+microbial+metabolites.">Bioactive microbial metabolites.</a> J. Antibiot. 58, 1-26 (2005).</li><li>Lopez, D., Vlamakis, H., 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=Generation+of+multiple+cell+types+in+Bacillus+subtilis.">Generation of multiple cell types in Bacillus subtilis.</a> FEMS Microbiol. Rev. 33, 152-163 (2009).</li><li>Vlamakis, H., Aguilar, C., Losick, R., 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=Control+of+cell+fate+by+the+formation+of+an+architecturally+complex+bacterial+community.">Control of cell fate by the formation of an architecturally complex bacterial community.</a> Genes Dev. 22, 945-953 (2008).</li><li>Branda, S. S., Gonzalez-Pastor, J. E., Ben-Yehuda, S., Losick, R., 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=Fruiting+body+formation+by+Bacillus+subtilis.">Fruiting body formation by Bacillus subtilis.</a> Proc. Natl. Acad. Sci. U.S.A. 98, 11621-11626 (2001).</li><li>Shank, E. A., 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=Interspecies+interactions+that+result+in+Bacillus+subtilis+forming+biofilms+are+mediated+mainly+by+members+of+its+own+genus.">Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus.</a> Proc. Natl. Acad. Sci. U.S.A. 108, 1236-1243 (2011).</li><li>Piston, D. W., Patterson, G. H., Lippincott-Schwartz, J., Claxton, N. S., Davidson, M. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Introduction to Fluorescent Proteins. , (2013).</li><li>Chudakov, D. M., Matz, M. V., Lukyanov, S., Lukyanov, K. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescent+proteins+and+their+applications+in+imaging+living+cells+and+tissues.">Fluorescent proteins and their applications in imaging living cells and tissues.</a> Physiol. Rev. 90, 1103-1163 (2010).</li><li>Shaner, N. C., Patterson, G. H., Davidson, M. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+fluorescent+protein+technology.">Advances in fluorescent protein technology.</a> J. Cell Sci. 120, 4247-4260 (2007).</li><li>Shaner, N. C., Steinbach, P. A., Tsien, R. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+guide+to+choosing+fluorescent+proteins.">A guide to choosing fluorescent proteins.</a> Nat. Methods. 2, 905-909 (2005).</li><li>Nicolas, P., 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=Condition-dependent+transcriptome+reveals+high-level+regulatory+architecture+in+Bacillus+subtilis.">Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.</a> Science. 335, 1103-1106 (2012).</li><li>Middleton, R., Hofmeister, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+shuttle+vectors+for+ectopic+insertion+of+genes+into+Bacillus+subtilis.">New shuttle vectors for ectopic insertion of genes into Bacillus subtilis.</a> Plasmid. 51, 238-245 (2004).</li><li>Shimotsu, H., Henner, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Construction+of+a+single-copy+integration+vector+and+its+use+in+analysis+of+regulation+of+the+trp+operon+of+Bacillus+subtilis.">Construction of a single-copy integration vector and its use in analysis of regulation of the trp operon of Bacillus subtilis.</a> Gene. 43, 85-94 (1986).</li><li>Guerout-Fleury, A. M., Frandsen, N., Stragier, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plasmids+for+ectopic+integration+in+Bacillus+subtilis.">Plasmids for ectopic integration in Bacillus subtilis.</a> Gene. 180, 57-61 (1996).</li><li>Semsey, S., Blaha, B., Koles, K., Orosz, L., Papp, P. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Site-specific+integrative+elements+of+rhizobiophage+16-3+can+integrate+into+proline+tRNA+(CGG)+genes+in+different+bacterial+genera.">Site-specific integrative elements of rhizobiophage 16-3 can integrate into proline tRNA (CGG) genes in different bacterial genera.</a> J. Bacteriol. 184, 177-182 (2002).</li><li>Charpentier, E., 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=Novel+cassette-based+shuttle+vector+system+for+gram-positive+bacteria.">Novel cassette-based shuttle vector system for gram-positive bacteria.</a> Appl. Environ. Microbiol. 70, 6076-6085 (2004).</li><li>Yang, H. Y., Kim, Y. W., Chang, H. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Construction+of+an+integration-proficient+vector+based+on+the+site-specific+recombination+mechanism+of+enterococcal+temperate+phage+phiFC1.">Construction of an integration-proficient vector based on the site-specific recombination mechanism of enterococcal temperate phage phiFC1.</a> J. Bacteriol. 184, 1859-1864 (2002).</li><li>Choi, K. H., Schweizer, H. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=mini-Tn7+insertion+in+bacteria+with+single+attTn7+sites:+example+Pseudomonas+aeruginosa.">mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa.</a> Nat. Protoc. 1, 153-161 (2006).</li><li>Craig, N. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tn7:+a+target+site-specific+transposon.">Tn7: a target site-specific transposon.</a> Mol. Microbiol. 5, 2569-2573 (1991).</li><li>Garcia-Betancur, J. C., Yepes, A., Schneider, J., Lopez, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+analysis+of+Bacillus+subtilis+biofilms+using+fluorescence+microscopy+and+flow+cytometry.">Single-cell analysis of Bacillus subtilis biofilms using fluorescence microscopy and flow cytometry.</a> J. Vis. Exp. (60), e3796 (2012).</li><li>Lopez, D., Fischbach, M. A., Chu, F., Losick, R., 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=Structurally+diverse+natural+products+that+cause+potassium+leakage+trigger+multicellularity+in+Bacillus+subtilis.">Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis.</a> Proc. Natl. Acad. Sci. U.S.A. 106, 280-285 (2009).</li><li>Vartoukian, S. R., Palmer, R. M., Wade, W. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Strategies+for+culture+of+'unculturable'+bacteria.">Strategies for culture of 'unculturable' bacteria.</a> FEMS Microbiol. Lett. 309, 1-7 (2010).</li><li>Romano, J. D., 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=Pseudomonas-Saccharomyces+interactions:+influence+of+fungal+metabolism+on+bacterial+physiology+and+survival.">Pseudomonas-Saccharomyces interactions: influence of fungal metabolism on bacterial physiology and survival.</a> J. Bacteriol. 187, 940-948 (2005).</li><li>Branda, S. S., Chu, F., Kearns, D. B., Losick, R., 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=A+major+protein+component+of+the+Bacillus+subtilis+biofilm+matrix.">A major protein component of the Bacillus subtilis biofilm matrix.</a> Mol. Microbiol. 59, 1229-1238 (2006).</li><li>Zengler, K., 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=Cultivating+the+uncultured.">Cultivating the uncultured.</a> Proc. Natl. Acad. Sci. U.S.A. 99, 15681-15686 (2002).</li></ol>

One of the inherent limitations of this protocol is that it relies on the cultivability of microbial organisms. As has been well documented24, most microbial life on the planet cannot (yet) be grown under the culturing conditions explored to date. Thus, a huge number of interactions between microbial species that are occurring in natural settings will go undetected using this approach. However, since our desire is to not only identify the existence of such interactions, but then also study the mechanisms and m...

We are interested in understanding how the metabolites that bacteria secrete affect the physiology and development of neighboring microbes. Many metabolites have been characterized for their bioactive effects on other microbes. Two well-described examples include antibiotics, which inhibit the growth of other microbes, and quorum sensing molecules, which alter the global gene expression of other microbes. However, bacteria produce many other small molecule natural products that have no known bioactivities1. We hypothesize that bacteria have evolved and preserved the ability to produce some of these metabolites because they allow them to modulate the cellular physiology of their microbial neighbors in the complex microbial communities within which most bacteria exist.
Bacillus subtilis cell types
We have focused our studies on chemically mediated microbial interactions that involve Bacillus subtilis. This is not only because of its status as the Gram-positive model bacterium and the resultant genetic tools available for its manipulation, but also because of its ability to differentiate into characterized cell types. Examples include cells that are: swimming; producing the extracellular matrix that is required for robust biofilm formation; competent to take up DNA from the environment; and sporulating, among others2. Each of these cell types expresses a characteristic transcriptional regulon that makes them physiologically and/or physically distinct from their genetically identical siblings. Under many growth conditions, multiple cell types coexist as various subpopulations within a single colony of B. subtilis cells3. Although many species of bacteria may exhibit analogous cell type heterogeneity, this phenomenon has been particularly well studied in B. subtilis.
In particular, genes that are upregulated within each of these specific B. subtilis cell types have been identified. Identifying such upregulated genes is essential for the work described here because many of these microbial phenotypes of interest are difficult or impossible to observe directly. For instance, we cannot visually detect a trait such as swimming on solid (1.5%) agar plates, even though a subpopulation of B. subtilis cells produce flagella under those conditions3. Another example is biofilm matrix-production. Matrix production can be visualized by colony morphology (as it results in macroscopically wrinkly colonies), but only on certain growth medium, and only after multiple days of growth4. However, by knowing which genes are upregulated during differentiation, we can construct transcriptional reporters that act as markers for cellular differentiation into these cell types.
Reporter constructs
These fluorescent transcriptional reporters consist of the promoters for cell-type specific genes driving the production of a reporter gene, for instance a fluorescent protein. Examples include Phag-yfp (for swimming cells), PtapA-yfp (for biofilm matrix-producing cells), and PsspB-yfp (for sporulating cells), where Px indicates the promoter region for gene x. These reporter constructs are integrated into a neutral locus on the chromosome (Figure 1 and see below) so that the native regulation of the phenotype is left intact. However, now when a cell expresses this phenotype, it also expresses a fluorescent protein. This provides an easily visualized read-out of the activation of particular phenotypic behavior, allowing us to screen for microbes that activate this physiological response. Although such reporters are commonly used in microbiology, they have not been broadly applied in screens to identify metabolic interactions between microbes before this method was described5.
There are a number of important considerations in the design and construction of cell-type-specific reporter strains. We have utilized exclusively transcriptional fluorescent reporters, although other types of constructs are certainly possible. We discourage the use of translational fusions as markers for cell type differentiation in our screen, however, for two reasons: 1) the desire to leave the native cell-type-specific protein unperturbed, and 2) the recognition that a diffuse, cell-wide fluorescence will be easier to detect than localized puncta within cells (common with translational fusions).
Reporter gene selection
After deciding to use transcription as a read-out, the reporter gene must be selected (e.g. LacZ, fluorescence, or luciferase). LacZ has the advantage of needing the least specialized equipment to detect, but there is a much higher likelihood of false positives among environmental microbes. In our hands, the background level of Lac+ organisms among soil microbes was prohibitively high (&#62;&#62;10% of soil microbes were blue (Lac+) on X-gal plates; data not shown). It is possible that by titrating the concentration of X-gal in the medium, this could be optimized to allow the use of an X-gal reporter, although we did not attempt this. Luciferase provides high sensitivity of detection and is the most orthogonal reporter: there is almost no chance of environmental microbes being inherently luminescent. However, we found it difficult to identify instrumentation at our institution that allowed luminescence detection across entire Petri plates, as most were designed to scan only localized regions in multi-well plates. There might also be complications in visualizing luminescent colonies in a manner that also allowed the simultaneous physical isolation of inducing organisms. While using fiduciaries may have made this possible, we instead elected to use fluorescent transcriptional reporters, which were proven to work in B. subtilis, provided adequate sensitivity of detection and low false positive rates among soil organisms, and allowed to use of easily available instrumentation for both visualization and isolation procedures.
Fluorophore selection
The specific fluorophore selected will depend on your bacterial species, the agar growth medium you are using, and the particular fluorescence filter sets you have available. With our instrumentation, we found that both the B. subtilis colonies themselves and the agar they were grown on exhibited less background fluorescence when YFP (yellow fluorescent protein) filters were used, making that reporter superior to GFP (green fluorescent protein) in our hands. The codon usage of fluorescent proteins are frequently optimized for eukaryotes, making it important to select a fluorophore either known from the literature to work in your bacterial species, or to test it explicitly using a constitutive promoter. A large number of ever-evolving fluorescent protein variants are currently available6, which have been reviewed in a number of sources7,8, some of which explicitly provide guidance on choosing an appropriate fluorescent protein for your experiment9.
Promoter selection
The selection of a promoter will largely depend on your cell type or phenotype of interest. For organisms such as B. subtilis, some cell-type specific reporter genes have been established in the literature. For other bacterial strains, examining microarray or transcriptional data will be necessary to provide information about which genes are highly upregulated under the conditions where your cell type of interest is manifested. A recent study cataloged the transcription of B. subtilis under 104 different growth conditions using tiling microarrays10. This paper provides comprehensive information about which genes are highly upregulated under different conditions, which is invaluable for less-well-characterized phenotypes.
Rather than mapping precise promoter regions for every gene of interest, we typically simply use the sequence 200-500 bp upstream of the gene as the promoter. The exact sequence length depends on the genomic context: shorter regions are used when necessary to avoid including upstream coding regions from neighboring open reading frames.
Neutral loci and integration
How to maintain the reporter construct in your bacterial strain becomes the final question in designing a fluorescent transcriptional reporter strain. In bacteria, genes of interest are frequently maintained on plasmids using antibiotic selection. However, it may not be possible to use antibiotics during coculture without killing the environmental microbes. If plasmids are stably maintained in your bacterial species, it may be possible grow your bacteria containing a plasmid-borne reporter in the presence of antibiotics to prepare your reporter for screening, and then eliminate antibiotics during the coculture itself in the hope that the plasmid will be sufficiently maintained to allow for fluorescence. However, if plasmids are easily lost in your bacterium, or are lost under stress conditions, this will not be a viable option. In many cases, the best solution will be to integrate the reporter construct onto the bacterial chromosome, which allows stable maintenance of the reporter even in the absence of selection. In order for the integration to not disrupt the normal expression or regulation of your gene of interest, we recommend integrating into an ectopic site on the chromosome that can act as a &#34;neutral locus.&#34; In B. subtilis these integration sites are genes that - when mutated - convey a phenotype in certain minimal media (allowing integrants to be identified without antibiotic selection), yet do not alter growth or sporulation rates in rich media, and include such genes as amyE , lacA, thrC , pyrD , gltA, and sacA (conveying the ability to utilize starch, &#946;-galactosides, threonine, uracil, glutamate, and sucrose, respectively)11-13 .
While integration in these genes have been used reliably for many years in B. subtilis (particularly at amyE and lacA), similar knowledge may not be available for genes in many other bacterial species. The use of phage attachment sites are great alternatives for neutral chromosomal integration sites: many species-specific14-16, as well as general integration sites such as the Tn7 attachment site (attTn7) have been identified and utilized for gene insertions in many bacterial species17,18.
Environmental microbes
We use soil as a direct source of environmental microbes for our coculture screen. The soil contains a high diversity of microbes, and many of these organisms are rich source of natural products. By using liquid suspensions of soil placed directly onto plates with our fluorescent transcriptional reporter strain (without prior isolation of bacteria from the soil), we greatly simplify the experimental approach. The soil can either be used immediately after harvesting, or be frozen at -80 &#176;C for future use. Immediate use has the advantage that a greater diversity of microbes can potentially be grown, including those that will not survive freezing well. It has the disadvantage that the concentration of cultivable soil organisms from these samples is unknown, increasing the number of screen plates that must be used. Delayed use has the advantage that the cfu/ml for each soil source can be determined in advance, allowing an optimized number of colonies to be grown on each screen plate. However, it requires that the soil organisms be capable of surviving freezing.
Note that diversifying the inducer pool being examined (i.e. the soil sources) appears to be more effective at identifying new interspecies interactions than in-depth screening on the same soil: greater phylogenetic diversity was observed in the hits identified in our matrix-induction screen as additional soil sources were examined rather than screening the same soil sources more thoroughly (E.A. Shank and R. Kolter, Harvard Medical School, unpublished results).
Overview
The approach we describe here is straightforward in terms of its technical requirements. It involves: 1) constructing a fluorescent transcriptional reporter in B. subtilis or another bacterial species of interest, 2) identifying conditions under which this reporter is not activated, 3) preparing aliquots of this reporter strain and organisms to be screened (in our case soil, but other sources could be utilized instead), 4) mixing these two sets of microbes on solid media, 5) identifying and isolating putative inducing organisms, and 6) confirming that these organisms do indeed activate this phenotype in a secondary screen. Once identified, these organisms and their metabolites provide us with chemical tools to modulate bacterial behavior, to study bacterial physiology and microbial interactions, and to potentially act as novel scaffolds for future therapeutic compounds.

<table border="1">
	<tbody>
		<tr>
			<td>Name of Reagent/ Equipment</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments/Description</td>
		</tr>
		<tr>
			<td>Spectrophotometer</td>
			<td></td>
			<td></td>
			<td>Any spectrophotomer capable of measuing OD600 absorbance values.</td>
		</tr>
		<tr>
			<td>Luria broth, Lennox</td>
			<td>VWR</td>
			<td>80017-484</td>
			<td>Alternative media sources may be necessary.</td>
		</tr>
		<tr>
			<td>Glass beads, 3 mm</td>
			<td>VWR</td>
			<td>26396-508</td>
			<td></td>
		</tr>
		<tr>
			<td>Gel loading tips, round</td>
			<td>VWR</td>
			<td>29442-666</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass rods</td>
			<td>VWR</td>
			<td>59060-069</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescence dissecting stereoscope</td>
			<td>Zeiss</td>
			<td>N/A</td>
			<td>The author used a Zeiss Stemi SV6 dissection stereoscope with an EXFO X-cite 120 fluorescent light source, a long-pass YFP filter cube, an achromat 0.63X objective, 10X eyepieces, and an Axio HRC HR digital camera. Most screening was done with the focusing mount at 2.0-3.2X. Any dissecting stereoscope with fluorescence capabilities is fine, provided you have the correct filters for the FP you are using. It is best if there is a shutter that allows you to easily switch between brightfield and fluorescense, as well as a stage that allows illumination from above and below. If you want to capture images, an attached camera is also necessary.</td>
		</tr>
	</tbody>
</table>

using coculture to detect chemically mediated interspecies interactions

In nature, bacteria rarely exist in isolation; they are instead surrounded by a diverse array of other microorganisms that alter the local environment by secreting metabolites. These metabolites have the potential to modulate the physiology and differentiation of their microbial neighbors and are likely important factors in the establishment and maintenance of complex microbial communities. We have developed a fluorescence-based coculture screen to identify such chemically mediated microbial interactions. The screen involves combining a fluorescent transcriptional reporter strain with environmental microbes on solid media and allowing the colonies to grow in coculture. The fluorescent transcriptional reporter is designed so that the chosen bacterial strain fluoresces when it is expressing a particular phenotype of interest (i.e. biofilm formation, sporulation, virulence factor production, etc.) Screening is performed under growth conditions where this phenotype is not expressed (and therefore the reporter strain is typically nonfluorescent). When an environmental microbe secretes a metabolite that activates this phenotype, it diffuses through the agar and activates the fluorescent reporter construct. This allows the inducing-metabolite-producing microbe to be detected: they are the nonfluorescent colonies most proximal to the fluorescent colonies. Thus, this screen allows the identification of environmental microbes that produce diffusible metabolites that activate a particular physiological response in a reporter strain. This publication discusses how to: a) select appropriate coculture screening conditions, b) prepare the reporter and environmental microbes for screening, c) perform the coculture screen, d) isolate putative inducing organisms, and e) confirm their activity in a secondary screen. We developed this method to screen for soil organisms that activate biofilm matrix-production in Bacillus subtilis; however, we also discuss considerations for applying this approach to other genetically tractable bacteria.

This screen was used to identify soil organisms secreting compounds that alter the physiology of B. subtilis. The results described here focus on the matrix-producing cell type of B. subtilis, which produces the protein and exopolysaccharide that are required for robust biofilm formation in this bacterium. We selected the promoter of the tapA-sipW-tasA operon for our fluorescent reporter construct (PtapA-yfp). This operon encodes the protein structural component of the matri...

Watch this Scientific Journal Video about Using Coculture to Detect Chemically Mediated Interspecies Interactions at JoVE.com

Using Coculture to Detect Chemically Mediated Interspecies Interactions

Bacteria produce secreted compounds that have the potential to affect the physiology of their microbial neighbors. Here we describe a coculture screen that allows detection of such chemically mediated interspecies interactions by mixing soil microbes with fluorescent transcriptional reporter strains of Bacillus subtilis on solid media.

In nature, bacteria rarely exist in isolation; they are instead surrounded by a diverse array of other microorganisms that alter the local environment by ...

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