Direct comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities

Yasmine Dergham, Dominique Coq, Pierre Nicolas, Elena Bidnenko, Sandra Dérozier, Maxime Deforet, Eugénie Huillet, Pilar Sanchez-Vizuete, Julien Deschamps, Kassem Hamze () and Romain Briandet ()
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Yasmine Dergham: INRAE, AgroParisTech, Micalis Institute
Dominique Coq: INRAE, AgroParisTech, Micalis Institute
Pierre Nicolas: Université Paris-Saclay, INRAE, MAIAGE
Elena Bidnenko: INRAE, AgroParisTech, Micalis Institute
Sandra Dérozier: Université Paris-Saclay, INRAE, MAIAGE
Maxime Deforet: Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin
Eugénie Huillet: INRAE, AgroParisTech, Micalis Institute
Pilar Sanchez-Vizuete: INRAE, AgroParisTech, Micalis Institute
Julien Deschamps: INRAE, AgroParisTech, Micalis Institute
Kassem Hamze: Lebanese University, Faculty of Science
Romain Briandet: INRAE, AgroParisTech, Micalis Institute

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: Abstract Bacillus subtilis can form various types of spatially organised communities on surfaces, such as colonies, pellicles and submerged biofilms. These communities share similarities and differences, and phenotypic heterogeneity has been reported for each type of community. Here, we studied spatial transcriptional heterogeneity across the three types of surface-associated communities. Using RNA-seq analysis of different regions or populations for each community type, we identified genes that are specifically expressed within each selected population. We constructed fluorescent transcriptional fusions for 17 of these genes, and observed their expression in submerged biofilms using time-lapse confocal laser scanning microscopy (CLSM). We found mosaic expression patterns for some genes; in particular, we observed spatially segregated cells displaying opposite regulation of carbon metabolism genes (gapA and gapB), indicative of distinct glycolytic or gluconeogenic regimes coexisting in the same biofilm region. Overall, our study provides a direct comparison of spatial transcriptional heterogeneity, at different scales, for the three main models of B. subtilis surface-associated communities.

Date: 2023
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DOI: 10.1038/s41467-023-43386-w

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