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Abstract The mechanisms by which two sister chromosomes separate and partition into daughter cells in bacteria remain poorly understood. A recent theoretical model has proposed that out-of-equilibrium processes associated with mRNA–ribosome (polysome) dynamics play a significant role in this process. Here we investigate the role of ribosomal dynamics on nucleoid segregation and separation inEscherichia coliusing high-throughput fluorescence microscopy in microfluidic devices. We compare our experimental observations with predictions from a reaction-diffusion model that includes the interactions among ribosomal subunits, polysomes, and chromosomal DNA. Our results show that the non-equilibrium behavior of mRNA and ribosomes causes them to aggregate at the midcell and this process contributes to the separation of the two daughter chromosomes. However, this effect is considerably weaker than that predicted by the model. Rather than relying solely on active mRNA–ribosome dynamics, our data suggest that the closing division septum via steric interactions and potentially entropic forces between two DNA strands coupled to cell elongation act as additional mechanisms to ensure faithful partitioning of the nucleoids to two daughter cells. SignificanceThe mitotic spindle separates chromosomes in eukaryotic cells, but bacteria lack this structure. It remains unclear how bacterial chromosomes partition prior to cell division. It has been hypothesized that non-equilibrium dynamics of polysomes, that is mRNA–ribosome complexes, actively drive the separation of bacterial chromosomes. Using quantitative microscopy combined with computational modeling, we show that polysome dynamics significantly contribute to chromosome segregation inEscherichia colibut this process does not constitute the sole mechanism. Our findings suggest the closing division septum via steric interactions and potentially entropic forces between two DNA strands act as additional mechanisms. 

Through their expansive mycelium network, soil fungi alter the physical arrangement and chemical composition of their local environment. This can significantly impact bacterial distribution and nutrient transport and can play a dramatic role in shaping the rhizosphere around a developing plant. However, direct observation and quantitation of such behaviors is extremely difficult due to the opacity and complex porosity of the soil microenvironment. In this study, we demonstrate the development and use of an engineered microhabitat to visualize fungal growth in response to varied levels of confinement. Microfluidics were fabricated using photolithography and conventional soft lithography, assembled onto glass slides, and prepared to accommodate fungal cultures. Selected fungal strains across three phyla (Ascomycota:Morchella sextalata,Fusarium falciforme; Mucoromycota:Linnemannia elongata,Podila minutissima,Benniella; Basidiomycota:Laccaria bicolor, andSerendipitasp.) were cultured within microhabitats and imaged using time-lapse microscopy to visualize development at the mycelial level. Fungal hyphae of each strain were imaged as they penetrated through microchannels with well-defined pore dimensions. The hyphal penetration rates through the microchannels were quantified via image analysis. Other behaviors, including differences in the degree of branching, peer movement, and tip strength were also recorded for each strain. Our results provide a repeatable and easy-to-use approach for culturing fungi within a microfluidics platform and for visualizing the impact of confinement on hyphal growth and other fungal behaviors pertinent to their remodeling of the underground environment. 

Abstract State-of-the-Art models of Root System Architecture (RSA) do not allow simulating root growth around rigid obstacles. Yet, the presence of obstacles can be highly disruptive to the root system. We grew wheat seedlings in sealed petri dishes without obstacle and in custom 3D-printed rhizoboxes containing obstacles. Time-lapse photography was used to reconstruct the wheat root morphology network. We used the reconstructed wheat root network without obstacle to calibrate an RSA model implemented in the R-SWMS software. The root network with obstacles allowed calibrating the parameters of a new function that models the influence of rigid obstacles on wheat root growth. Experimental results show that the presence of a rigid obstacle does not affect the growth rate of the wheat root axes, but that it does influence the root trajectory after the main axis has passed the obstacle. The growth recovery time, i.e. the time for the main root axis to recover its geotropism-driven growth, is proportional to the time during which the main axis grows along the obstacle. Qualitative and quantitative comparisons between experimental and numerical results show that the proposed model successfully simulates wheat RSA growth around obstacles. Our results suggest that wheat roots follow patterns that could inspire the design of adaptive engineering flow networks.