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<p>Dynamic social interactions within bacterial biofilms drive distinct spatial organisation and transcriptional responses. Here, we combine fluorescence <i>in situ</i> hybridisation (FISH), confocal laser scanning microscopy (CLSM), and RNA sequencing (RNA-Seq) to investigate a model three-species biofilm community derived from a dairy pasteuriser, comprising <i>Stenotrophomonas rhizophila</i>, <i>Microbacterium lacticum</i>, and <i>Bacillus licheniformis</i>. CLSM revealed species-specific biovolume dynamics and stratified 3D structures over 24&#xa0;h, with <i>S. rhizophila</i> as the dominant species and <i>M. lacticum</i> exhibiting the lowest abundance yet playing an essential role as the initial coloniser. Spatial patterns reflected known pairwise interactions – commensalism, exploitation, and neutral interaction. Transcriptomic profiling of <i>S. rhizophila</i> revealed extensive gene expression changes in dual-species biofilms with <i>M. lacticum</i>, including upregulation of genes related to flagellar motility, nutrient acquisition, energy metabolism, and TonB-dependent transport. In contrast, co-culture with <i>B. licheniformis</i> induced minimal transcriptional changes in <i>S. rhizophila</i>, consistent with a neutral interaction among the two. Our findings demonstrate how interspecies interactions govern both spatial topology and functional specialisation in mixed-species biofilms which is of relevance to microbial ecology, industrial biofilm control, and the targeting of keystone biofilm species.</p>

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Microbial Interactions Shape Spatial Organisation and Transcriptional Responses in a Model Mixed-Species Biofilm

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月2日

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  • Faizan Ahmed Sadiq,
  • Nan Yang,
  • Jenten Goeteyn,
  • Koen De Reu,
  • Marc Heyndrickx,
  • Mette Burmølle

摘要

Dynamic social interactions within bacterial biofilms drive distinct spatial organisation and transcriptional responses. Here, we combine fluorescence in situ hybridisation (FISH), confocal laser scanning microscopy (CLSM), and RNA sequencing (RNA-Seq) to investigate a model three-species biofilm community derived from a dairy pasteuriser, comprising Stenotrophomonas rhizophila, Microbacterium lacticum, and Bacillus licheniformis. CLSM revealed species-specific biovolume dynamics and stratified 3D structures over 24 h, with S. rhizophila as the dominant species and M. lacticum exhibiting the lowest abundance yet playing an essential role as the initial coloniser. Spatial patterns reflected known pairwise interactions – commensalism, exploitation, and neutral interaction. Transcriptomic profiling of S. rhizophila revealed extensive gene expression changes in dual-species biofilms with M. lacticum, including upregulation of genes related to flagellar motility, nutrient acquisition, energy metabolism, and TonB-dependent transport. In contrast, co-culture with B. licheniformis induced minimal transcriptional changes in S. rhizophila, consistent with a neutral interaction among the two. Our findings demonstrate how interspecies interactions govern both spatial topology and functional specialisation in mixed-species biofilms which is of relevance to microbial ecology, industrial biofilm control, and the targeting of keystone biofilm species.