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RNAseq reveals that Pseudomonas aeruginosa mounts medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia

ABSTRACT: Most habitats on earth are colonized by diverse bacterial communities, offering ample opportunities for inter-species interactions. While competition for space and nutrients might often dominate such interactions, little is known about whether bacteria can sense competitors and mount specific responses to withstand their attacks. The competition-sensing hypothesis proposes that bacteria can do so through nutrient stress and cell damage cues. Here, we conducted a replicated RNAseq-transcriptomic study to test this hypothesis. We exposed Pseudomonas aeruginosa to either its own spent medium or to the supernatant of its competitor Burkholderia cenocepacia. Compared to controls, we detected significant changes in the transcriptome of P. aeruginosa that entail both general responses to spent medium and specific responses to the competitor. Specifically, genes encoding various competitive traits, including the type-VI secretion system, the siderophore pyoverdine, and the toxins phenazines and hydrogen cyanide, were upregulated when exposed to the competitor supernatant. Similarly, several stress response and quorum-sensing regulators were overexpressed. Moreover, we found transcriptional responses to vary as a function of iron availability, whereby metabolically more costly responses were launched under iron rich conditions. Altogether, our results reveal nuanced competitive responses of P. aeruginosa when exposed to B. cenocepacia supernatant, integrating both environmental and social cues.

ORGANISM(S): Pseudomonas aeruginosa PAO1

PROVIDER: GSE224821 | GEO | 2023/12/31

REPOSITORIES: GEO

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Project description:BACKGROUND: Hundreds of bacterial species coexist within the human oral cavity, where complex interactions can occur. Recent evidence has shown that the commensal oral streptococci that populate supragingival biofilms on the tooth surface produce extracellular proteases that degrade cell-cell signaling molecules of their disease-causing competitors, Streptococcus mutans. To further explore these interactions, we performed transcriptome analysis of S. mutans cocultured with different oral streptococci and found that cell-cell signaling was complety inhibited, but only when the bacteria were directly cocultured together. METHODS: RNA-Seq was utilized to compare the transcriptomes of S. mutans wild-type strain UA159 cocultured in its own supernatant (3 replicates), UA159 cocultured in S. sp. A12 supernatant (3 replicates) and directly cocultured with S. sp. A12 (3 replicates). Strains were grown to OD600 nm = 0.5 in CDM medium before harvest. Deep sequencing was performed at the University of Florida ICBR facilities (Gainesville, FL). Approximately 15 million short-reads were obtained for each sample. After removing adapter sequences from each short-read and trimming of the 3’-ends by quality scores, the resulting sequences were mapped onto the reference genome of strain UA159 (GenBank accession no. AE014133) using the short-read aligner. Mapped short-read alignments were then converted into readable formats using SAMTOOLS. RESULTS: Using an optimzed data analysis workflow, we mapped 13-16 million reads per sample to the genome of UA159. For viewing of the mapped reads aligned to the genome, .bam files were uploaded into the Integrative Genomics Viewer (IGV – version 2.3.55). A .csv file containing raw read counts for each replicate (3) was then uploaded to Degust (http://degust.erc.monash.edu/) and edgeR analysis performed to determine Log2 fold change and a false discovery rate (FDR). When comparing the growth of S. mutans in its own spent supernatant against competitor spent supernatants, we found 88 genes differentially expressed (Log2 fold change > (-)1.5, -log10 P-value > 4) which included upregulation of the zinc transport system and several amino acid ABC transporters, along with downregulation of the TnSmu1 genomic island. A more substantial effect was seen when we compared growth of S. mutans in competitor spent supernatant compared to growth directly with a competitor. Here, 140 genes were differentially expressed and included upregulation of one of the CRISPR genetic clusters as well as downregulation of the entire genetic competence regulon, as expected. Principal component analysis (PCA) of transcriptome data from these three conditions displayed a wide variation and separation among the tested groups, further confirming a unique transcriptome response for S. mutans between growth in the supernatant of a competitor and directly with a competitor. CONCLUSIONS: We believe that these measured transcriptomic changes represent a conserved S. mutans response to competitors that has not been previously captured in RNA-Seq experiments of monocultures alone. Together, these results highlight a previously undocumented transcriptomic alteration by S. mutans when challenged by health-associated oral streptococci.

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RNAseq reveals that Pseudomonas aeruginosa mounts medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia

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