title: Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing.
abstract: Comparative genomics, metagenomics, and single-cell technologies have shown that populations of microbial species encompass assemblages of closely related strains. This raises the question of whether individual bacterial lineages respond to the presence of their close relatives by modifying their gene expression or, instead, whether assemblages simply act as the arithmetic addition of their individual components. Here, we took advantage of transcriptome sequencing to address this question. For this, we analyzed the transcriptomes of two closely related strains of the extremely halophilic bacterium Salinibacter ruber grown axenically and in coculture. These organisms dominate bacterial assemblages in hypersaline environments worldwide. The strains used here cooccurred in the natural environment and are 100% identical in their 16S rRNA genes, and each strain harbors an accessory genome representing 10% of its complete genome. Overall, transcriptomic patterns from pure cultures were very similar for both strains. Expression was detected along practically the whole genome albeit with some genes at low levels. A subset of genes was very highly expressed in both strains, including genes coding for the light-driven proton pump xanthorhodopsin, genes involved in the stress response, and genes coding for transcriptional regulators. Expression differences between pure cultures affected mainly genes involved in environmental sensing. When the strains were grown in coculture, there was a modest but significant change in their individual transcription patterns compared to those in pure culture. Each strain sensed the presence of the other and responded in a specific manner, which points to fine intraspecific transcriptomic modulation.
authors.affiliation: Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: González-Torres
authors.affiliation: Bioinformatics and Genomics Program, Centre for Genomic Regulation, Barcelona, Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Leszek P
authors.initials: LP
authors.lastname: Pryszcz
authors.affiliation: Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Santos
authors.affiliation: Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Martínez-García
authors.affiliation: Bioinformatics and Genomics Program, Centre for Genomic Regulation, Barcelona, Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain tgabaldon@crg.es anton@ua.es.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain Multidisciplinary Institute of Environmental Studies Ramon Margalef, University of Alicante, Alicante, Spain tgabaldon@crg.es anton@ua.es.
authors.forename: Josefa
authors.initials: J
authors.lastname: Antón
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D041963:Bacteroidetes / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D018920:Coculture Techniques; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics; D056265:Microbial Interactions / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D025604:Rhodopsins, Microbial / Q000235:genetics; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D025604:Rhodopsins, Microbial; C519152:xanthorhodopsin, Salinibacter