Interactions between Closely Related Bacterial Strains Are Revealed by Deep Transcriptome Sequencing

Abstract

e 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. Bacterial species appear in nature as assemblages of closely related strains with extensive genetic heterogeneity, as revealed by comparative genomic analyses of isolates, metagenomics, and, more recently, single-cell genome analyses (1). However, data from genomic analyses of individual genomes from isolated representatives are inconclusive with respect to the ecological and functional significance of this variation, given that subtle genetic variations can lead to distinct ecological strategies (2, 3). In addition, genetic inventories per se are only lists of the capabilities of bacteria and do not provide information on their actual behavior in nature.Salinibacter ruber is an extremely halophilic bacterium of the phylum Bacteroidetes that is present in hypersaline environments worldwide. Its discovery changed the paradigm that only extremely halophilic Archaea could thrive in close-to-saturation hypersaline environments and provided the first example of a member of the domain Bacteria for which ecological relevance in these systems could be proven. Studies of the large collection of strains of S. ruber isolated from around the world as well as metagenomic studies have shown that this species, while being highly homogeneous from a phylogenetic standpoint, harbors very wide genomic microdive...

Molecular processes underlying synergistic linuron mineralization in a triple‐species bacterial consortium biofilm revealed by differential transcriptomics

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Coculturing Bacteria Leads to Reduced Phenotypic Heterogeneities

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Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence ofV. choleraeduring co-infection with ETEC

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