More Like this

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. 

   more » « less
2. Stranger than metals

   https://doi.org/10.1126/science.abh4273  

   Phillips, Philip W. ; Hussey, Nigel E. ; Abbamonte, Peter ( July 2022 , Science)

   BACKGROUND Landau’s Fermi liquid theory provides the bedrock on which our understanding of metals has developed over the past 65 years. Its basic premise is that the electrons transporting a current can be treated as “quasiparticles”—electron-like particles whose effective mass has been modified, typically through interactions with the atomic lattice and/or other electrons. For a long time, it seemed as though Landau’s theory could account for all the many-body interactions that exist inside a metal, even in the so-called heavy fermion systems whose quasiparticle mass can be up to three orders of magnitude heavier than the electron’s mass. Fermi liquid theory also lay the foundation for the first successful microscopic theory of superconductivity. In the past few decades, a number of new metallic systems have been discovered that violate this paradigm. The violation is most evident in the way that the electrical resistivity changes with temperature or magnetic field. In normal metals in which electrons are the charge carriers, the resistivity increases with increasing temperature but saturates, both at low temperatures (because the quantized lattice vibrations are frozen out) and at high temperatures (because the electron mean free path dips below the smallest scattering pathway defined by the lattice spacing). In “strange metals,” by contrast, no saturation occurs, implying that the quasiparticle description breaks down and electrons are no longer the primary charge carriers. When the particle picture breaks down, no local entity carries the current. ADVANCES A new classification of metallicity is not a purely academic exercise, however, as strange metals tend to be the high-temperature phase of some of the best superconductors available. Understanding high-temperature superconductivity stands as a grand challenge because its resolution is fundamentally rooted in the physics of strong interactions, a regime where electrons no longer move independently. Precisely what new emergent phenomena one obtains from the interactions that drive the electron dynamics above the temperature where they superconduct is one of the most urgent problems in physics, attracting the attention of condensed matter physicists as well as string theorists. One thing is clear in this regime: The particle picture breaks down. As particles and locality are typically related, the strange metal raises the distinct possibility that its resolution must abandon the basic building blocks of quantum theory. We review the experimental and theoretical studies that have shaped our current understanding of the emergent strongly interacting physics realized in a host of strange metals, with a special focus on their poster-child: the copper oxide high-temperature superconductors. Experiments are highlighted that attempt to link the phenomenon of nonsaturating resistivity to parameter-free universal physics. A key experimental observation in such materials is that removing a single electron affects the spectrum at all energy scales, not just the low-energy sector as in a Fermi liquid. It is observations of this sort that reinforce the breakdown of the single-particle concept. On the theoretical side, the modern accounts that borrow from the conjecture that strongly interacting physics is really about gravity are discussed extensively, as they have been the most successful thus far in describing the range of physics displayed by strange metals. The foray into gravity models is not just a pipe dream because in such constructions, no particle interpretation is given to the charge density. As the breakdown of the independent-particle picture is central to the strange metal, the gravity constructions are a natural tool to make progress on this problem. Possible experimental tests of this conjecture are also outlined. OUTLOOK As more strange metals emerge and their physical properties come under the scrutiny of the vast array of experimental probes now at our disposal, their mysteries will be revealed and their commonalities and differences cataloged. In so doing, we should be able to understand the universality of strange metal physics. At the same time, the anomalous nature of their superconducting state will become apparent, offering us hope that a new paradigm of pairing of non-quasiparticles will also be formalized. The correlation between the strength of the linear-in-temperature resistivity in cuprate strange metals and their corresponding superfluid density, as revealed here, certainly hints at a fundamental link between the nature of strange metallicity and superconductivity in the cuprates. And as the gravity-inspired theories mature and overcome the challenge of projecting their powerful mathematical machinery onto the appropriate crystallographic lattice, so too will we hope to build with confidence a complete theory of strange metals as they emerge from the horizon of a black hole. Curved spacetime with a black hole in its interior and the strange metal arising on the boundary. This picture is based on the string theory gauge-gravity duality conjecture by J. Maldacena, which states that some strongly interacting quantum mechanical systems can be studied by replacing them with classical gravity in a spacetime in one higher dimension. The conjecture was made possible by thinking about some of the fundamental components of string theory, namely D-branes (the horseshoe-shaped object terminating on a flat surface in the interior of the spacetime). A key surprise of this conjecture is that aspects of condensed matter systems in which the electrons interact strongly—such as strange metals—can be studied using gravity. 

   more » « less
3. Biofilms on plastic litter in an urban river: Community composition and activity vary by substrate type

   https://doi.org/10.1002/wer.11008  

   Lazcano, Raúl F. ; Kelly, John J. ; Hoellein, Timothy J. ( March 2024 , Water Environment Research)

   In aquatic ecosystems, plastic litter is a substrate for biofilms. Biofilms on plastic and natural surfaces share similar composition and activity, with some differences due to factors such as porosity. In freshwaters, most studies have examined biofilms on benthic substrates, while little research has compared the activity and composition of biofilms on buoyant plastic and natural surfaces. Additionally, the influence of substrate size and successional stage on biofilm composition has not been commonly assessed. We incubated three plastics of distinct textures that are buoyant in rivers, low‐density polyethylene (rigid; 1.7 mm thick), low‐density polyethylene film (flexible; 0.0254 mm thick), and foamed polystyrene (brittle; 6.5 mm thick), as well as wood substrates (untreated oak veneer; 0.6 mm thick) in the Chicago River. Each material was incubated at three sizes (1, 7.5, and 15 cm²). Substrates were incubated at 2–10 cm depths and removed weekly for 6 weeks. On each substrate we measured chlorophyll concentration, biofilm biomass, respiration, and flux of nitrogen gas. We sequenced 16S and 23S rRNA genes at Weeks 1, 3, and 6 to capture biofilm community composition across successional stages. Chlorophyll, biomass, and N₂flux were similar across substrates, but respiration was greater on wood than plastics. Bacterial and algal richness and diversity were highest on foam and wood compared to polyethylene substrates. Bacterial biofilm community composition was distinct between wood and plastic substrates, while the algal community was distinct on wood and foam, which were different from each other and polyethylene substrates. These results indicate that polymer properties influence biofilm alpha and beta diversity, which may affect transport and distribution of plastic pollution and associated microbes, as well as biogeochemical processes in urban rivers. This study provides valuable insights into the effects of substrate on biofilm characteristics, and the ecological impacts of plastic pollution on urban rivers.

   Plastic physical and chemical properties act as forces of selection for biofilm.

   Biofilm activity was similar among three different types of plastic.

   Community composition between plastic and wood was different.

    

   more » « less
4. Mechanical instability and interfacial energy drive biofilm morphogenesis

   https://doi.org/10.7554/eLife.43920  

   Yan, Jing ; Fei, Chenyi ; Mao, Sheng ; Moreau, Alexis ; Wingreen, Ned S ; Košmrlj, Andrej ; Stone, Howard A ; Bassler, Bonnie L ( March 2019 , eLife)

   Engineers have long studied how mechanical instabilities cause patterns to form in inanimate materials, and recently more attention has been given to how such forces affect biological systems. For example, stresses can build up within a tissue if one layer grows faster than an adjacent layer. The tissue can release this stress by wrinkling, folding or creasing. Though ancient and single-celled, bacteria can also develop spectacular patterns when they exist in the lifestyle known as a biofilm: a community of cells adhered to a surface. But do mechanical instabilities drive the patterns seen in biofilms? To investigate, Yan, Fei, Mao et al. grew biofilms of the bacterium called Vibrio cholerae – which causes the disease cholera – on solid, non-growing ‘substrates’. This work revealed that as the biofilms grow, their expansion is constrained by the substrate, and this situation generates mechanical stresses. To release the stresses, the biofilm initially folds to form wrinkles. Later, as the biofilm expands further, small parts of it detach from the substrate to form blisters. The same forces that keep water droplets spherical (known as interfacial forces) dictate how the blisters evolve, interact, and eventually shape the expanding biofilm. Using these principles, Yan et al. could engineer the biofilm into desired shapes. Collectively, the results presented by Yan et al. connect the shape of the biofilm surface with its material properties, in particular its stiffness. Understanding this relationship could help researchers to develop new ways to remove harmful biofilms, such as those that cause disease or that damage underwater structures. The stiffness of biofilms is already known to affect how well bacteria can resist antibiotics. Future studies could look for new genes or compounds that change the material properties of a biofilm, thereby altering the biofilm surface. 

   more » « less
5. Antibiotic Susceptibility of Escherichia coli Cells during Early-Stage Biofilm Formation

   https://doi.org/10.1128/JB.00034-19  

   Gu, Huan ; Lee, Sang Won ; Carnicelli, Joseph ; Jiang, Zhaowei ; Ren, Dacheng ; O'Toole, George ( September 2019 , Journal of Bacteriology)

   ABSTRACT Bacteria form complex multicellular structures on solid surfaces known as biofilms, which allow them to survive in harsh environments. A hallmark characteristic of mature biofilms is the high-level antibiotic tolerance (up to 1,000 times) compared with that of planktonic cells. Here, we report our new findings that biofilm cells are not always more tolerant to antibiotics than planktonic cells in the same culture. Specifically, Escherichia coli RP437 exhibited a dynamic change in antibiotic susceptibility during its early-stage biofilm formation. This phenomenon was not strain specific. Upon initial attachment, surface-associated cells became more sensitive to antibiotics than planktonic cells. By controlling the cell adhesion and cluster size using patterned E. coli biofilms, cells involved in the interaction between cell clusters during microcolony formation were found to be more susceptible to ampicillin than cells within clusters, suggesting a role of cell-cell interactions in biofilm-associated antibiotic tolerance. After this stage, biofilm cells became less susceptible to ampicillin and ofloxacin than planktonic cells. However, when the cells were detached by sonication, both antibiotics were more effective in killing the detached biofilm cells than the planktonic cells. Collectively, these results indicate that biofilm formation involves active cellular activities in adaption to the attached life form and interactions between cell clusters to build the complex structure of a biofilm, which can render these cells more susceptible to antibiotics. These findings shed new light on bacterial antibiotic susceptibility during biofilm formation and can guide the design of better antifouling surfaces, e.g., those with micron-scale topographic structures to interrupt cell-cell interactions. IMPORTANCE Mature biofilms are known for their high-level tolerance to antibiotics; however, antibiotic susceptibility of sessile cells during early-stage biofilm formation is not well understood. In this study, we aim to fill this knowledge gap by following bacterial antibiotic susceptibility during early-stage biofilm formation. We found that the attached cells have a dynamic change in antibiotic susceptibility, and during certain phases, they can be more sensitive to antibiotics than planktonic counterparts in the same culture. Using surface chemistry-controlled patterned biofilm formation, cell-surface and cell-cell interactions were found to affect the antibiotic susceptibility of attached cells. Collectively, these findings provide new insights into biofilm physiology and reveal how adaptation to the attached life form may influence antibiotic susceptibility of bacterial cells. 

   more » « less