Biology subjects

Deforet, M.

Publications and source records attributed to Deforet, M..

7 recordsLinked to original sources

bioRxiv2026

Toolbox for fluorescent labelling of Pseudomonas aeruginosa across scales: from single cells to bacterial communities and host infection models

Fluorescence microscopy is central to the study of bacterial cell biology, multicellular behaviours, and host-pathogen interactions. Bright, robust and photostable labelling is required for bacterial identification, sorting and quantitative analysis, driving continuous development of state-of-the-art labelling tools. Here, we developed a multicolor fluorescent cell labelling toolkit for Gram-negative bacteria carrying the attTn7 site, using the opportunistic human pathogen Pseudomonas aeruginosa as a model. Cell labelling is achieved by constitutive chromosomal expression of genes encoding a choice of four novel fluorescent proteins, mNeonGreen, mJuniper, mLychee and mScarlet-I3, codon-optimised for P. aeruginosa. These reporters provide bright, stable fluorescence with minimal photobleaching and excellent spectral separation during long-term imaging of single cells, macrocolonies and biofilms. Chromosomal expression of mNeonGreen yielded brighter and more homogeneous labelling than expression of the same construct from a plasmid. Importantly, dual-color labelling of macrocolonies uncovered previously unrecognised phenomena of collective motility when two isogenic swarming populations interact. Finally, we demonstrate the applicability of our constructs in biologically relevant host-pathogen contexts by imaging both live and fixed P. aeruginosa-infected human airway epithelial cells. This versatile cell labelling platform enables reliable bacterial identification, segmentation, tracking, and quantitative fluorescence imaging across spatial and temporal scales, and is readily adaptable to most other Gram-negative bacteria as the attTn7 integration site is well conserved.

microbiology↗

bioRxiv2022

The rhamnolipids of Pseudomonas aeruginosa change the mechanical properties of biogels

Pseudomonas aeruginosa makes and secretes massive amounts of rhamnolipid surfactants that enable swarming motility over biogel surfaces. But how this rhamnolipids interact with biogels to assist swarming remains unclear. Here I use a combination of optical techniques across scales and genetically-engineered strains to demonstrate that rhamnolipids can induce agar gel swelling over distances > 10,000x the body size of an individual cell. The swelling front is on the micrometric scale, and is easily visible using shadowgraphy. Rhamnolipid transport is not restricted to the surface of the gel, but occurs through the whole thickness of the plate and, consequently, the spreading dynamics depends on the local thickness. Surprisingly, rhamnolipids can cross the whole gel and induce swelling on the opposite side of a two-face Petri dish. The swelling front delimits an area where the mechanical properties of the surface properties are modified: water wets the surface more easily, which increases the motility of individual bacteria and enables collective motility. A genetically-engineered mutant unable to secrete rhamnolipids (DrhlA), and therefore unable to swarm, is rescued from afar with rhamnolipids produced by a remote colony. These results exemplify the remarkable capacity of bacteria to change the physical environment around them and its ecological consequences. Significance statementLiving organisms have the ability to interact mechanically with their environment. Pseudomonas aeruginosa, a motile bacterium, can spread collectively on biogels, a behavior called swarming. Rhamnolipids, surfactant molecules P. aeruginosa make and secrete, are required for swarming. Here, I demonstrate rhamnolipids not only physically alter the biogel in the vicinity of the secreting cells, but also over distances much greater than the bacterial cell size, through gel swelling. This long-distance physical alteration can even rescue a remote colony which would not produce rhamnolipids. This work illustrates the remarkable ability of bacteria to change the mechanical property of the world surrounding them.

systems biology↗

bioRxiv2022

FLAGELLAR MOTILITY DURING E. COLI BIOFILM FORMATION PROVIDES A COMPETITIVE DISADVANTAGE WHICH RECEDES IN THE PRESENCE OF CO-COLONIZERS.

In nature, bacteria form biofilms in very diverse environments, involving a range of specific properties and exhibiting competitive advantages for surface colonization. However, the underlying mechanisms are difficult to decipher. In particular, the contribution of cell flagellar motility to biofilm formation remains unclear. Here, we examined the ability of motile and nonmotile E. coli cells to form a biofilm in a well-controlled geometry, both in a simple situation involving a single-species biofilm and in the presence of co-colonizers. Using a millifluidic channel, we determined that motile cells have a clear disadvantage in forming a biofilm, exhibiting a long delay as compared to nonmotile cells. By monitoring biofilm development in real time, we observed that the decisive impact of flagellar motility on biofilm formation consists in the alteration of surface access time. Implementing a simple mathematical model to calculate surface access velocity for both motile (diffusion) and nonmotile (settling) cells, we discovered that the competitive advantage strongly depends on the geometry of the environment to be colonized. Interestingly, this advantage reverts for the smallest geometries, with a crossover at a height of 100 m. We also report that the difference between and nonmotile cells in the ability to form a biofilm diminishes in the presence of cocolonizers, which could be due to motility inhibition through the consumption of key resources by the co-colonizers. We conclude that the impact of flagellar motility on surface colonization closely depends on the environment geometry and the population features, suggesting a unifying vision of the role of cell motility in surface colonization and biofilm formation.

microbiology↗

bioRxiv2020

Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma

In melanoma, transcriptional profiling has revealed multiple co-existing cell states, including proliferative versus invasive sub-populations that have been posited to represent a "go or grow" tradeoff. Both of these populations are maintained in tumors, but how they physically interact to promote metastasis is unknown. We demonstrate that these subpopulations form spatially structured heterotypic clusters that cooperate in the seeding of metastasis. We unexpectedly found that INV cells were tightly adherent to each other, and formed clusters with a rim of PRO cells. Intravital imaging demonstrated cooperation between these populations, in which the INV cells facilitated the spread of less metastatic PRO cells. We identified the TFAP2 neural crest transcription factor as a master regulator of both clustering and the PRO/INV states. Our data suggest a framework for the co-existence of these two divergent cell populations, in which differing cell states form heterotypic clusters that promote metastasis via cell-cell cooperation.

cancer biology↗

bioRxiv2020

Open Science Saves Lives: Lessons from the COVID-19 Pandemic

In the last decade Open Science principles have been successfully advocated for and are being slowly adopted in different research communities. In response to the COVID-19 pandemic many publishers and researchers have sped up their adoption of Open Science practices, sometimes embracing them fully and sometimes partially or in a sub-optimal manner. In this article, we express concerns about the violation of some of the Open Science principles and its potential impact on the quality of research output. We provide evidence of the misuses of these principles at different stages of the scientific process. We call for a wider adoption of Open Science practices in the hope that this work will encourage a broader endorsement of Open Science principles and serve as a reminder that science should always be a rigorous process, reliable and transparent, especially in the context of a pandemic where research findings are being translated into practice even more rapidly. We provide all data and scripts at https://osf.io/renxy/.

scientific communication and education↗

bioRxiv2020

Spatial-temporal dynamics of a microbial cooperative behavior robust to cheating

Individuals living in dense populations control their behaviors by sensing, integrating and responding to many cues. How can these processes enable the evolution and stability of cooperative behaviors that could easily be exploited by cheaters? Here we shed light on how bacteria regulate cooperation by studying swarming in Pseudomonas aeruginosa, a behavior requiring cooperative secretions of rhamnolipid surfactants to facilitate collective movement over surfaces. By combining fluorescent imaging and computational analyses we show, counterintuitively, that rhamnolipid expression peaks at swarming edges. We then show that the integration of competing diffusive cues--quorum sensing signals and growth-limiting nutrients--enables P. aeruginosa to communicate across centimeters and adopt expression patterns unseen in well-mixed liquid culture. Integration of multiple cues enables robustness against cheating even when we experimentally perturb the quorum sensing system. Taken together, these results illuminate how the integration of cues in spatially structured communities can stabilize cooperation.

systems biology↗

bioRxiv2017

A simple rule for the evolution of fast dispersal at the edge of expanding populations

Predicting evolution of expanding populations is critical to control biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of evolution where organisms pay a reproductive cost to disperse faster. When does selection favor this survival of the fastest? We searched for a simple rule, motivated by evolution experiments where swarming bacteria evolved into an hy-perswarmer mutant which disperses[~] 100% faster but pays a growth cost of [~] 10% to make many copies of its flagellum. We analyzed a two-species model based on the Fisher equation to explain this observation: the population expansion rate (v) results from an interplay of growth (r) and dispersal (D) and is independent of the carrying capacity: [Formula]. A mutant can take over the edge only if its expansion rate (v2) exceeds the expansion rate of the established species (v1); this simple condition (v2 > v1) determines the maximum cost in slower growth that a faster mutant can pay and still be able to take over. Numerical simulations and time-course experiments where we tracked evolution by imaging bacteria suggest that our findings are general: less favorable conditions delay but do not entirely prevent the success of the fastest. Thus, the expansion rate defines a traveling wave fitness, which could be combined with trade-offs to predict evolution of expanding populations.

evolutionary biology↗