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1. Quorum Sensing and Antimicrobial Production Orchestrate Biofilm Dynamics in Multispecies Bacterial Communities

   https://doi.org/10.1128/spectrum.02615-22  

   Armes, April C.; Walton, Jillian L.; Buchan, Alison (October 2022, Microbiology Spectrum)

   DeAngelis, Kristen M. (Ed.)

   ABSTRACT Microbial interactions are often mediated by diffusible small molecules, including secondary metabolites, that play roles in cell-to-cell signaling and inhibition of competitors. Biofilms are often “hot spots” for high concentrations of bacteria and their secondary metabolites, which make them ideal systems for the study of small-molecule contributions to microbial interactions. Here, we use a five-member synthetic community consisting of Roseobacteraceae representatives to investigate the role of secondary metabolites on microbial biofilm dynamics. One synthetic community member, Rhodobacterales strain Y4I, possesses two acylated homoserine lactone (AHL)-based cell-to-cell signaling systems ( pgaRI and phaRI ) as well as a nonribosomal peptide synthase gene ( igi ) cluster that encodes the antimicrobial indigoidine. Through serial substitution of Y4I with mutants deficient in single signaling molecule pathways, the contribution of these small-molecule systems could be assessed. As secondary metabolite production is dependent upon central metabolites, the influence of growth substrate (i.e., complex medium versus defined medium with a single carbon substrate) on these dynamics was also considered. Depending on the Y4I mutant genotype included, community dynamics ranged from competitive to cooperative. The observed interactions were mostly competitive in nature. However, the community harboring a Y4I variant that was both impaired in quorum sensing (QS) pathways and unable to produce indigoidine ( pgaR variant) shifted toward more cooperative interactions over time. These cooperative interactions were enhanced in the defined growth medium. The results presented provide a framework for deciphering complex, small-molecule-mediated interactions that have broad application to microbial biology. IMPORTANCE Microbial biofilms play critical roles in marine ecosystems and are hot spots for microbial interactions that play a role in the development and function of these communities. Roseobacteraceae are an abundant and active family of marine heterotrophic bacteria forming close associations with phytoplankton and carrying out key transformations in biogeochemical cycles. Group members are aggressive primary colonizers of surfaces, where they set the stage for the development of multispecies biofilm communities. Few studies have examined the impact of secondary metabolites, such as cell-to-cell signaling and antimicrobial production, on marine microbial biofilm community structure. Here, we assessed the impact of secondary metabolites on microbial interactions using a synthetic, five-member Roseobacteraceae community by measuring species composition and biomass production during biofilm growth. We present evidence that secondary metabolites influence social behaviors within these multispecies microbial biofilms, thereby improving understanding of bacterial secondary metabolite production influence on social behaviors within marine microbial biofilm communities. 

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2. Effects of fluid shear stress on oral biofilm formation and composition and the transcriptional response of Streptococcus gordonii

   https://doi.org/10.1111/omi.12481  

   Nairn, Brittany_L; Lima, Bruno_P; Chen, Ruoqiong; Yang, Judy_Q; Wei, Guanju; Chumber, Ashwani_K; Herzberg, Mark_C (August 2024, Molecular Oral Microbiology)

   Abstract Biofilms are subjected to many environmental pressures that can influence community structure and physiology. In the oral cavity, and many other environments, biofilms are exposed to forces generated by fluid flow; however, our understanding of how oral biofilms respond to these forces remains limited. In this study, we developed a linear rocker model of fluid flow to study the impact of shear forces onStreptococcus gordoniiand dental plaque‐derived multispecies biofilms. We observed that as shear forces increased,S. gordoniibiofilm biomass decreased. Reduced biomass was largely independent of overall bacterial growth. Transcriptome analysis ofS. gordoniibiofilms exposed to moderate levels of shear stress uncovered numerous genes with differential expression under shear. We also evaluated an ex vivo plaque biofilm exposed to fluid shear forces. LikeS. gordonii, the plaque biofilm displayed decreased biomass as shear forces increased. Examination of plaque community composition revealed decreased diversity and compositional changes in the plaque biofilm exposed to shear. These studies help to elucidate the impact of fluid shear on oral bacteria and may be extended to other bacterial biofilm systems. 

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3. Diffusiophoretic Particle Penetration into Bacterial Biofilms .

   Somasundar, A. (June 2023, ACS applied materials interfaces)

   Bacterial biofilms are communities of cells adhered to surfaces. These communities represent a predominant form of bacterial life on Earth. A defining feature of a biofilm is the three-dimensional extracellular polymer matrix that protects resident cells by acting as a mechanical barrier to the penetration of chemicals, such as antimicrobials. Beyond being recalcitrant to antibiotic treatment, biofilms are notoriously difficult to remove from surfaces. A promising, but relatively under explored approach to biofilm control, is to disrupt the extracellular polymer matrix by enabling penetration of particles to increase the susceptibility of biofilms to antimicrobials. In this work, we investigate externally imposed chemical gradients as a mechanism to transport polystyrene particles into bacterial biofilms. We show that pre-conditioning the biofilm with a pre-wash step using deionized (DI) water is essential for altering the biofilm so it takes up the micro- and nanoparticles by the application of a further chemical gradient created by an electrolyte. Using different particles and chemicals, we document the transport behavior that leads to particle motion into the biofilm and its further reversal out of the biofilm. Our results demonstrate the importance of chemical gradients in disrupting the biofilm matrix, regulating particle transport in crowded macromolecular environments, and suggest potential applications of particle transport and delivery in other physiological systems. 

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4. Synthesis of Metal‐Modified Nanocellulose as a Biofilm Analogue for Biofilm Mimicry in Biomedical and Environmental Applications

   https://doi.org/10.1002/bip.70029  

   Taylor, Darryl_W; Jones, III, A‐Andrew_D (May 2025, Biopolymers)

   ABSTRACT Bacterial biofilms are complex, multi‐component structures consisting primarily of four key elements: polysaccharides, metal ions, proteins, and extracellular DNA. In our research, we specifically focus on the polysaccharide and metal ion components, which play a crucial role in determining the biofilm's mechanical properties. Polysaccharides provide the structural matrix, although metal ions, particularly divalent cations like calcium and cobalt, cross‐link with the polysaccharides, thereby modulating the biofilm's rigidity and viscoelastic behavior. By introducing divalent cations into nanocellulose, we can replicate this natural cross‐linking process, allowing us to finely tune the material's mechanical properties to more closely resemble those of bacterial biofilms. This approach not only enhances the accuracy of synthetic biofilm models over alginate hydrogels but also provides valuable insights into how biofilms maintain their structural integrity in various environments. Our findings indicate that nanocellulose exhibits mechanical properties closer to biofilms than alginate analogs, making it a suitable non‐living control for biofilm studies. Furthermore, divalent nickel, followed by calcium and magnesium, demonstrate a closer mechanical mimicry to biofilms. In conclusion, this research shows the potential of nanocellulose as a versatile material for bacterial biofilm mimicry. 

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5. Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates

   https://doi.org/10.1073/pnas.1919607117  

   Fei, Chenyi; Mao, Sheng; Yan, Jing; Alert, Ricard; Stone, Howard A.; Bassler, Bonnie L.; Wingreen, Ned S.; Košmrlj, Andrej (March 2020, Proceedings of the National Academy of Sciences)

   During development, organisms acquire three-dimensional (3D) shapes with important physiological consequences. While basic mechanisms underlying morphogenesis are known in eukaryotes, it is often difficult to manipulate them in vivo. To circumvent this issue, here we present a study of developingVibrio choleraebiofilms grown on agar substrates in which the spatiotemporal morphological patterns were altered by varying the agar concentration. Expanding biofilms are initially flat but later undergo a mechanical instability and become wrinkled. To gain mechanistic insights into this dynamic pattern-formation process, we developed a model that considers diffusion of nutrients and their uptake by bacteria, bacterial growth/biofilm matrix production, mechanical deformation of both the biofilm and the substrate, and the friction between them. Our model shows quantitative agreement with experimental measurements of biofilm expansion dynamics, and it accurately predicts two distinct spatiotemporal patterns observed in the experiments—the wrinkles initially appear either in the peripheral region and propagate inward (soft substrate/low friction) or in the central region and propagate outward (stiff substrate/high friction). Our results, which establish that nonuniform growth and friction are fundamental determinants of stress anisotropy and hence biofilm morphology, are broadly applicable to bacterial biofilms with similar morphologies and also provide insight into how other bacterial biofilms form distinct wrinkle patterns. We discuss the implications of forming undulated biofilm morphologies, which may enhance the availability of nutrients and signaling molecules and serve as a “bet hedging” strategy. 

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