Article
Microbiology
Tianyi Chen, Meng Pu, Sundharraman Subramanian, Dan Kearns, Dean Rowe-Magnus
Summary: Elevated c-di-GMP levels inhibit the swimming motility of Vibrio vulnificus and promote biofilm formation, aggregation, and oyster colonization, while attenuating its virulence in mice.
Article
Multidisciplinary Sciences
Calvin K. Lee, William C. Schmidt, Shanice S. Webster, Jonathan W. Chen, George A. O'Toole, Gerard C. L. Wong
Summary: This study reveals that changes in c-di-GMP levels in bacterial biofilms are not the sole factor determining surface commitment, as oscillations in c-di-GMP levels can propagate across generations. Additionally, the study demonstrates that modulation of c-di-GMP signals and cooperative surface commitment can be influenced by varying the interaction strength between PilO and SadC.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Yiquan Zhang, Yue Qiu, He Gao, Junfang Sun, Xue Li, Miaomiao Zhang, Xingfan Xue, Wenhui Yang, Bin Ni, Lingfei Hu, Zhe Yin, Renfei Lu, Dongsheng Zhou
Summary: The master QS regulator OpaR in Vibrio parahaemolyticus directly regulates a group of genes to impact the concentration of c-di-GMP, which in turn influences behaviors such as biofilm formation. This direct association between QS and c-di-GMP metabolism allows for precise control of gene transcription and bacterial behaviors.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Siying Lin, Shuzhen Chen, Li Li, Huiluo Cao, Ting Li, Ming Hu, Lisheng Liao, Lian-Hui Zhang, Zeling Xu
Summary: This study characterized a uropathogenic Pseudomonas aeruginosa strain, PA_HN002, and found that its high intracellular c-di-GMP content contributed to enhanced biofilm formation. Analysis of the c-di-GMP metabolizing enzymes in PA_HN002 revealed multiple mutations in phosphodiesterases (PDEs), which resulted in a shifted expression profile and elevated intracellular c-di-GMP levels, promoting biofilm production.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zhuo Wang, Xiaorong Xie, Daohan Shang, Laigong Xie, Yueyue Hua, Li Song, Yantao Yang, Yao Wang, Xihui Shen, Lei Zhang
Summary: Cellular c-di-GMP levels play an important role in regulating bacterial behaviors such as motility, biofilm formation, and virulence. This study reveals a regulatory cascade in Burkholderia thailandensis that controls the cellular level of c-di-GMP. PdcA, PdcB, and PdcC constitute an operon, and PdcA acts as a diguanylate cyclase (DGC) that is inhibited by phosphorylated PdcC. PdcB dephosphorylates PdcC to derepress the activity of PdcA. This c-di-GMP regulatory model is found to be widespread in the Proteobacteria phylum.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Claudia A. Cox, Marek Bogacz, Faiha M. El Abbar, Darren D. Browning, Brian Y. Hsueh, Chris M. Waters, Vincent T. Lee, Stuart A. Thompson
Summary: Campylobacter jejuni is a leading cause of bacterial gastroenteritis and is associated with various extragastrointestinal conditions. The study found that CbrR is a negative regulator that controls motility and the expression of FlaA, a critical virulence factor in C. jejuni pathogenesis.
Article
Microbiology
Courtney N. Dial, Steven J. Eichinger, Randi Foxall, Christopher J. Corcoran, Alice H. Tischler, Robert M. Bolz, Cheryl A. Whistler, Karen L. Visick
Summary: Bacterial motility is crucial for the symbiotic colonization of the squid Euprymna scolopes by Vibrio fischeri, with strain KB2B1 exhibiting a unique migration pattern compared to ES114, possibly due to mutations in the quorum sensing pathway and DGC gene. The mutations shifted KB2B1 to a perceived low cell density state and inhibited migration, highlighting differences in regulatory control between strains.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Courtney N. Dial, Lauren Speare, Garrett C. Sharpe, Scott M. Gifford, Alecia N. Septer, Karen L. Visick
Summary: Vibrio fischeri efficiently colonizes its squid host by producing a transient biofilm dependent on symbiosis polysaccharide. Yeast extract inhibits biofilm formation, while omitting it and adding vitamin pABA and calcium can induce biofilm formation. pABA increases the concentration of c-di-GMP, which plays a crucial role in inducing biofilm formation.
Article
Environmental Sciences
April C. Armes, Alison Buchan
Summary: The study provides genetic evidence that the two QS systems in Rhodobacterales sp. Y4I work hierarchically to coordinate the production of the antimicrobial indigoidine and biofilm formation. The QS2 system, pgaRI, is shown to be at the top of the regulatory hierarchy governing indigoidine biosynthesis, while QS1 system, phaRI, influences biofilm development. Additionally, c-di-GMP levels are altered in QS and indigoidine biosynthesis Y4I mutants, indicating its integration into the QS circuitry of this strain.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Immunology
Yiran Yang, Weisheng Li, Ya Li, Weibo Shi, Jinxia Zhang, Wei Dang, Weiwei Zhang
Summary: This study quantitatively determined and morphologically characterized the biofilm formation of V. splendidus. It observed three stages of biofilm formation: adhesion, aggregation, and maturation. The inhibitory effect of exogenous c-di-GMP on the biofilm formation of V. splendidus was determined. Proteomic analysis was performed to explore the preliminary inhibitory mechanism of exogenous c-di-GMP on the biofilm formation of V. splendidus.
MICROBIAL PATHOGENESIS
(2023)
Review
Biotechnology & Applied Microbiology
Xiaobo Liu, Bin Cao, Liang Yang, Ji-Dong Gu
Summary: Biofilm formation and biofilm-induced biodeterioration have significant impacts on the community. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a key signaling molecule in bacteria, regulating various bacterial processes. Understanding the regulatory mechanisms of c-di-GMP would benefit the control of bacterial processes and the development of anti-biofilm technologies.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Biotechnology & Applied Microbiology
Xiaojun Zhong, Zhong Lu, Fei Wang, Ning Yao, Mengting Shi, Menghua Yang
Summary: This study identified a novel protein, GefA, in Vibrio parahaemolyticus that regulates bacterial behaviors and virulence. It was also shown that flagella participate in the infection of this bacterium, and GefA plays a crucial role in regulating bacterial virulence. This research contributes to a better understanding of the function of c-di-GMP and its synthetases in V. parahaemolyticus.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Xiao-Xiao Gong, Yan-Hua Zeng, Hai-Min Chen, Na Zhang, Yue Han, Hao Long, Zhen-Yu Xie
Summary: This study found that c-di-GMP metabolic proteins can regulate different phenotypic outputs in Vibrio alginolyticus, a dominant marine pathogen, and overexpression of certain proteins enhances biofilm matrix production. The high abundance of c-di-GMP metabolic proteins suggests the importance of c-di-GMP signaling in the response and adaptation of V. alginolyticus to the marine environment. This work provides a foundation for further research on the molecular mechanisms of c-di-GMP in biofilm formation.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Keila Belhart, Federico Sisti, Monica C. Gestal, Julieta Fernandez
Summary: Bordetella bronchiseptica is a gram-negative bacterium that serves as a model for studying host-pathogen interactions. This study identifies the diguanylate cyclase BdcB as an important regulator of biofilm formation and motility in B. bronchiseptica. The absence of BdcB leads to increased cytotoxicity and pro-inflammatory response in macrophages, as well as upregulation of T3SS-mediated toxins. These findings highlight the role of BdcB in virulence regulation and host immune response in B. bronchiseptica.
SCIENTIFIC REPORTS
(2023)
Article
Environmental Sciences
Xing Fan Xue, Miao Miao Zhang, Jun Fang Sun, Xue Li, Qu Min Wu, Zhe Yin, Wen Hui Yang, Bin Ni, Ling Fei Hu, Dong Sheng Zhou, Ren Fei Lu, Yi Quan Zhang
Summary: The study revealed that the H-NS gene negatively regulates biofilm formation in Vibrio parahaemolyticus RIMD2210633, possibly through repression of intracellular c-di-GMP production.
BIOMEDICAL AND ENVIRONMENTAL SCIENCES
(2022)
Article
Geosciences, Multidisciplinary
Uria Alcolombri, Francois J. Peaudecerf, Vicente I. Fernandez, Lars Behrendt, Kang Soo Lee, Roman Stocker
Summary: Laboratory experiments and modeling suggest that faster sinking rates can significantly enhance bacterial degradation of organic particles in the ocean, due to the flow-induced removal of waste products. This mechanism may have a broad occurrence in natural marine conditions.
Article
Multidisciplinary Sciences
Jen Nguyen, Vicente Fernandez, Sammy Pontrelli, Uwe Sauer, Martin Ackermann, Roman Stocker
Summary: The study reveals that bacterial growth rates can decrease up to 50% when facing nutrient fluctuations with periods as short as 30 seconds to 60 minutes, compared to a stable nutrient environment with equal average concentration. The unique growth response of cells exposed to fluctuating nutrient environments contributes to a 38% reduction in growth rate, suggesting an unexpected adaptation to fluctuations in nutrient availability.
NATURE COMMUNICATIONS
(2021)
Article
Environmental Sciences
Yang Yue, Jingru Cheng, Kang Soo Lee, Roman Stocker, Xu He, Maosheng Yao, Jing Wang
Summary: This study investigated the formation mechanism and influencing factors of sulfate in fine particles during haze episodes in different city environments through experiments and collected samples. The results revealed that relative humidity significantly affects the formation of new CaSO4.2H2O crystals.
ATMOSPHERIC ENVIRONMENT
(2022)
Article
Engineering, Environmental
Jonathan E. Hunter, Helen F. Fredricks, Lars Behrendt, Uria Alcolombri, Shavonna M. Bent, Roman Stocker, Benjamin A. S. Van Mooy
Summary: The study reveals hidden lipidomic heterogeneity in natural particulate organic matter (POM) and phytoplankton cells, with new insights into the sources and degradation of lipids in sinking particles. Individual diatom cells from a single culture show marked lipid heterogeneity, indicating fundamental mechanisms underlying cell division. These findings suggest that even phytoplankton cell cultures should be viewed as mixtures of physiologically distinct populations.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Biophysics
Noele Norris, Uria Alcolombri, Johannes M. Keegstra, Yutaka Yawata, Filippo Menolascina, Emilio Frazzoli, Naomi M. Levine, Vicente Fernandez, Roman Stocker
Summary: This study investigates how E. coli senses and responds to gradients of maltose. The researchers found that the abundance of a specific porin protein limits the uptake of maltose into the periplasm, allowing E. coli to sense micromolar gradients of maltose despite having a high-affinity ABC transport system that is saturated at these levels. The study suggests a trade-off between uptake and sensing, with high-affinity transport enabling higher uptake rates but severely limiting the range of dynamic sensing.
BIOPHYSICAL JOURNAL
(2022)
Article
Multidisciplinary Sciences
Jean-Baptiste Raina, Bennett S. Lambert, Donovan H. Parks, Christian Rinke, Nachshon Siboni, Anna Bramucci, Martin Ostrowski, Brandon Signal, Adrian Lutz, Himasha Mendis, Francesco Rubino, Vicente I. Fernandez, Roman Stocker, Philip Hugenholtz, Gene W. Tyson, Justin R. Seymour
Summary: This study demonstrates the chemotactic responses of marine bacteria and archaea towards microscale hotspots of phytoplankton-derived dissolved organic matter (DOM). The specific chemical cues attract different prokaryotic populations, which play important roles in biogeochemical processes and ecological interactions in the marine food web.
Review
Microbiology
Johannes M. Keegstra, Francesco Carrara, Roman Stocker
Summary: The mechanism of bacterial chemotaxis is well understood, but the reasons and consequences behind it are still puzzling. Besides foraging, bacterial chemotaxis also plays alternative ecological roles such as navigation, localization, and promoting microbial diversity. Most insights on chemotaxis are obtained from laboratory studies, and observing individual and collective migratory behavior of bacteria in different environments can provide a better understanding of the trade-offs between chemotaxis and growth. Further research using in situ approaches and transgenerational tracking is needed to explore the role of chemotaxis in microbial life.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Eleonora Secchi, Giovanni Savorana, Alessandra Vitale, Leo Eberl, Roman Stocker, Roberto Rusconi
Summary: It has been found that the mechanical stability of Pseudomonas aeruginosa streamers mainly relies on the presence of extracellular DNA (eDNA) and the exopolysaccharide Pel. Controlling the composition of streamers can effectively control the formation of biofilm structures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Trang T. H. Nguyen, Emily J. Zakem, Ali Ebrahimi, Julia Schwartzman, Tolga Caglar, Kapil Amarnath, Uria Alcolombri, Francois J. Peaudecerf, Terence Hwa, Roman Stocker, Otto X. Cordero, Naomi M. Levine
Summary: Micro-scale microbial community dynamics significantly impact the fate of sinking particles in the ocean, playing a crucial role in global carbon cycling and future climate. By scaling-up essential features of particle-associated microbial dynamics, this study provides mechanistic insight into the contribution of microbes to the vertical carbon flux in the ocean.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Vicente Fernandez, Roman Stocker, Gabriel Juarez
Summary: Immiscible hydrocarbons in the ocean water column occur as droplets of varying diameters. The relationship between droplet size distribution and oil degradation rates by bacteria is unclear. The use of chemical dispersants in oil spill response is based on the assumption that increasing the surface-area-to-volume ratio of droplets will enhance biodegradation rates, but this argument doesn't hold in most natural marine environments. A mechanistic encounter-consumption model predicts the characteristic time for oil degradation by marine bacteria, taking into account the initial oil concentration, droplet size distribution, and the abundance of oil-degrading bacteria. The model shows that reducing droplet size below an optimum can increase the persistence of oil droplets in the environment.
SCIENTIFIC REPORTS
(2022)
Article
Ecology
Soren Hallstrom, Jean-Baptiste Raina, Martin Ostrowski, Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz, Roman Stocker, Justin R. Seymour, Lasse Riemann
Summary: Heterotrophic bacterial diazotrophs (HBDs) in the pelagic ocean can use chemotaxis to locate low-oxygen microenvironments suitable for nitrogen fixation, and their activity can influence marine nitrogen and carbon biogeochemistry.
Article
Physics, Multidisciplinary
Giovanni Savorana, Steffen Geisel, Tianyu Cen, Yuya Ling, Roman Stocker, Roberto Rusconi, Eleonora Secchi
Summary: This article investigates the effect of polymer solutions on bacterial transport in fluid flow. Microfluidic experiments and numerical modeling show that an increase in viscosity reduces bacterial depletion in low-shear regions of Newtonian solutions, while non-Newtonian solutions exhibit depletion similar to buffer solutions despite having higher viscosity.
FRONTIERS IN PHYSICS
(2022)
Article
Biochemical Research Methods
Soeren Ahmerkamp, Farooq Moin Jalaluddin, Yuan Cui, Douglas R. Brumley, Cesar O. Pacherres, Jasmine S. Berg, Roman Stocker, Marcel M. M. Kuypers, Klaus Koren, Lars Behrendt
Summary: This study presents sensPIV, a method for simultaneously measuring O2 concentrations and flow fields. By tracking O2-sensitive microparticles in fluid, the researchers measured O2 transport within microfluidic devices, sinking model aggregates, and complex colony-forming corals, and found that corals use ciliary movement to link zones of photosynthetic O2 production to zones of O2 consumption.
CELL REPORTS METHODS
(2022)
Article
Chemistry, Physical
Giovanni Savorana, Jonasz Slomka, Roman Stocker, Roberto Rusconi, Eleonora Secchi
Summary: This study presents a microfluidic platform for the reproducible growth and characterization of biofilm streamers. The platform allows for the analysis of biochemical composition, morphology, and rheology of the streamers. Additionally, a protocol for in situ hydrodynamic stress tests was developed to investigate the role of fluid shear stress on the structure and rheology of streamers.
Article
Biochemical Research Methods
Roberto Pioli, Miguel Angel Fernandez-Rodriguez, Fabio Grillo, Laura Alvarez, Roman Stocker, Lucio Isa, Eleonora Secchi
Summary: This new microfluidic platform utilizes capillary forces to deposit individual particles into traps microfabricated onto a substrate, allowing for the generation of desired spatial layouts of colloidal particles. The platform can create various patterns and easily allows surface functionalization of trapped particles, demonstrating an easy-to-build platform for use in microfluidics labs.