More Like this

1. Differential coping strategies exerted by biofilm and planktonic cells of Bacillus subtilis in response to a protozoan predator

   https://doi.org/10.1128/spectrum.01597-25  

   Kolodkin-Gal, Ilana; Murugan, Prem Anand; Mahapatra, Smruti; Zanditenas, Eva; Ankri, Serge (January 2026, Microbiology Spectrum)

   Carabetta, Valerie Jean (Ed.)

   The human protozoan parasite Entamoeba histolytica causes amebiasis and interacts with both beneficial and harmful members of the microbiome. In previous studies, it was shown that E. histolytica can break down pre-established biofilms of Bacillus subtilis in a time- and dose-dependent manner. Inhibiting parasitic cysteine proteases impairs biofilm degradation. However, it is still unknown whether bacteria can sense this process and respond to the degradation of the biofilms. Here, our research demonstrates a multilayered response of probiotic bacteria to the parasite, which differs between planktonic bacteria and pre-established biofilms. Sensing the activity of cysteine proteases from E. histolytica, the bacteria activate the general stress response and, to a lesser extent, the cell wall stress response. This activation helps the surviving members of the biofilm become more resistant to mild stressors such as ethanol, hydrogen peroxide, and sub-mic concentrations of ampicillin. On the other hand, planktonic cells exposed to the predators’ lysate deactivate the expression of genes associated with biofilm formation while inducing their motility to avoid predation. Overall, our results indicate that bacteria have evolved to recognize amoeba predators capable of degrading biofilms. Furthermore, the partially digested biofilm cells may have unexpected disadvantages over bacteria that did not encounter a predator. These findings may be useful in developing more efficient probiotic strains that are resilient to amebiasis. 

   more » « less
2. Breakdown of clonal cooperative architecture in multispecies biofilms and the spatial ecology of predation

   https://doi.org/10.1073/pnas.2212650120  

   Wucher, Benjamin R.; Winans, James B.; Elsayed, Mennat; Kadouri, Daniel E.; Nadell, Carey D. (February 2023, Proceedings of the National Academy of Sciences)

   Biofilm formation, including adherence to surfaces and secretion of extracellular matrix, is common in the microbial world, but we often do not know how interaction at the cellular spatial scale translates to higher-order biofilm community ecology. Here we explore an especially understudied element of biofilm ecology, namely predation by the bacteriumBdellovibrio bacteriovorus. This predator can kill and consume many different Gram-negative bacteria, includingVibrio choleraeandEscherichia coli.V. choleraecan protect itself from predation within densely packed biofilm structures that it creates, whereasE. colibiofilms are highly susceptible toB. bacteriovorus. We explore how predator–prey dynamics change whenV. choleraeandE. coliare growing in biofilms together. We find that in dual-species prey biofilms,E. colisurvival underB. bacteriovoruspredation increases, whereasV. choleraesurvival decreases.E. colibenefits from predator protection when it becomes embedded within expanding groups of highly packedV. cholerae. But we also find that the ordered, highly packed, and clonal biofilm structure ofV. choleraecan be disrupted ifV. choleraecells are directly adjacent toE. colicells at the start of biofilm growth. When this occurs, the two species become intermixed, and the resulting disordered cell groups do not block predator entry. Because biofilm cell group structure depends on initial cell distributions at the start of prey biofilm growth, the surface colonization dynamics have a dramatic impact on the eventual multispecies biofilm architecture, which in turn determines to what extent both species survive exposure toB. bacteriovorus. 

   more » « less
3. Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria

   https://doi.org/10.1128/mSystems.00877-19  

   Simmons, Emilia L.; Bond, Matthew C.; Koskella, Britt; Drescher, Knut; Bucci, Vanni; Nadell, Carey D. (June 2020, mSystems)

   Bordenstein, Seth (Ed.)

   ABSTRACT Encounters among bacteria and their viral predators (bacteriophages) are among the most common ecological interactions on Earth. These encounters are likely to occur with regularity inside surface-bound communities that microbes most often occupy in natural environments. Such communities, termed biofilms, are spatially constrained: interactions become limited to near neighbors, diffusion of solutes and particulates can be reduced, and there is pronounced heterogeneity in nutrient access and physiological state. It is appreciated from prior theoretical work that phage-bacteria interactions are fundamentally different in spatially structured contexts, as opposed to well-mixed liquid culture. Spatially structured communities are predicted to promote the protection of susceptible host cells from phage exposure, and thus weaken selection for phage resistance. The details and generality of this prediction in realistic biofilm environments, however, are not known. Here, we explore phage-host interactions using experiments and simulations that are tuned to represent the essential elements of biofilm communities. Our simulations show that in biofilms, phage-resistant cells—as their relative abundance increases—can protect clusters of susceptible cells from phage exposure, promoting the coexistence of susceptible and phage-resistant bacteria under a large array of conditions. We characterize the population dynamics underlying this coexistence, and we show that coexistence is recapitulated in an experimental model of biofilm growth measured with confocal microscopy. Our results provide a clear view into the dynamics of phage resistance in biofilms with single-cell resolution of the underlying cell-virion interactions, linking the predictions of canonical theory to realistic models and in vitro experiments of biofilm growth. IMPORTANCE In the natural environment, bacteria most often live in communities bound to one another by secreted adhesives. These communities, or biofilms, play a central role in biogeochemical cycling, microbiome functioning, wastewater treatment, and disease. Wherever there are bacteria, there are also viruses that attack them, called phages. Interactions between bacteria and phages are likely to occur ubiquitously in biofilms. We show here, using simulations and experiments, that biofilms will in most conditions allow phage-susceptible bacteria to be protected from phage exposure, if they are growing alongside other cells that are phage resistant. This result has implications for the fundamental ecology of phage-bacteria interactions, as well as the development of phage-based antimicrobial therapeutics. 

   more » « less
4. Microfluidic investigation of the impacts of flow fluctuations on the development of Pseudomonas putida biofilms

   https://doi.org/10.1038/s41522-023-00442-z  

   Wei, Guanju; Yang, Judy Q. (December 2023, npj Biofilms and Microbiomes)

   Abstract Biofilms play critical roles in wastewater treatment, bioremediation, and medical-device-related infections. Understanding the dynamics of biofilm formation and growth is essential for controlling and exploiting their properties. However, the majority of current studies have focused on the impact of steady flows on biofilm growth, while flow fluctuations are common in natural and engineered systems such as water pipes and blood vessels. Here, we reveal the effects of flow fluctuations on the development ofPseudomonas putidabiofilms through systematic microfluidic experiments and the development of a theoretical model. Our experimental results showed that biofilm growth under fluctuating flow conditions followed three phases: lag, exponential, and fluctuation phases. In contrast, biofilm growth under steady-flow conditions followed four phases: lag, exponential, stationary, and decline phases. Furthermore, we demonstrated that low-frequency flow fluctuations promoted biofilm growth, while high-frequency fluctuations inhibited its development. We attributed the contradictory impacts of flow fluctuations on biofilm growth to the adjustment time (T₀) needed for biofilm to grow after the shear stress changed from high to low. Furthermore, we developed a theoretical model that explains the observed biofilm growth under fluctuating flow conditions. Our insights into the mechanisms underlying biofilm development under fluctuating flows can inform the design of strategies to control biofilm formation in diverse natural and engineered systems. 

   more » « less
5. A biophysical threshold for biofilm formation

   https://doi.org/10.7554/eLife.76380  

   Moore-Ott, Jenna A; Chiu, Selena; Amchin, Daniel B; Bhattacharjee, Tapomoy; Datta, Sujit S (June 2022, eLife)

   Bacteria are ubiquitous in our daily lives, either as motile planktonic cells or as immobilized surface-attached biofilms. These different phenotypic states play key roles in agriculture, environment, industry, and medicine; hence, it is critically important to be able to predict the conditions under which bacteria transition from one state to the other. Unfortunately, these transitions depend on a dizzyingly complex array of factors that are determined by the intrinsic properties of the individual cells as well as those of their surrounding environments, and are thus challenging to describe. To address this issue, here, we develop a generally-applicable biophysical model of the interplay between motility-mediated dispersal and biofilm formation under positive quorum sensing control. Using this model, we establish a universal rule predicting how the onset and extent of biofilm formation depend collectively on cell concentration and motility, nutrient diffusion and consumption, chemotactic sensing, and autoinducer production. Our work thus provides a key step toward quantitatively predicting and controlling biofilm formation in diverse and complex settings. 

   more » « less