Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from studies of antibiotic efficacy to investigations of growth under different nutritional or stress environments, to characterization of different mutant strains, including those harbouring synthetic circuits. OD measurements are performed under the assumption that the OD value obtained is proportional to the cell number, i.e. the concentration of the sample. However, the assumption holds true in a limited range of conditions, and calibration techniques that determine that range are currently missing. Here we present a set of calibration procedures and considerations that are necessary to successfully estimate the cell concentration from OD measurements.

How a single bacterium becomes a colony of many thousand cells is important in biomedicine and food safety. Much is known about the molecular and genetic bases of this process, but less about the underlying physical mechanisms. Here we study the growth of single-layer micro-colonies of rod-shaped Escherichia coli bacteria confined to just under the surface of soft agarose by a glass slide. Analysing this system as a liquid crystal, we find that growth-induced activity fragments the colony into microdomains of well-defined size, whilst the associated flow orients it tangentially at the boundary. Topological defect pairs with charges are produced at a constant rate, with the defects being propelled to the periphery. Theoretical modelling suggests that these phenomena have different physical origins from similar observations in other extensile active nematics, and a growing bacterial colony belongs to a new universality class, with features reminiscent of the expanding universe.

Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from studies of antibiotic efficacy to investigations of growth under different nutritional or stress environments, to characterization of different mutant strains, including those harbouring synthetic circuits. OD measurements are performed under the assumption that the OD value obtained is proportional to the cell number, i.e. the concentration of the sample. However, the assumption holds true in a limited range of conditions, and calibration techniques that determine that range are currently missing. Here we present a set of calibration procedures and considerations that are necessary to successfully estimate the cell concentration from OD measurements.Bacteria and yeast are widely studied microorganisms of great economic, medical and societal interest. Much of our understanding of bacterial and yeast life cycles stems from monitoring their proliferation in time and the most routine way of doing so is using optical density (OD) measurements. The applications of such measurements range from routine checks during different cloning techniques 1 ; through studying cellular physiology and metabolism 2,3 ; to determining the growth rate for antibiotic dosage 4,5 ; and monitoring of biomass accumulation during bio-industrial fermentation 6 . Here we introduce a set of calibration techniques that take into account the relevant parameters affecting OD measurements, including at high culture densities, in a range of conditions commonly used by researchers.OD measurements have become synonymous with measurements of bacterial number (N) or concentration (C), in accordance with the Beer-Lambert law. However, OD measurements are turbidity measurements 7,8 , thus the Beer-Lambert law can be applied, with some considerations, only for microbial cultures of low densities. OD measurements in plate readers, increasingly used for high-throughput estimates of microbial growth, operate predominantly at higher culture densities where OD is expected to have a parabolic dependency on N 8 . Additionally, the proportionality constants (either in low or high density regimes) strongly depend on several parameters, for example cell size, which need to be included in robust calibration techniques. Yet, these techniques, essential when using OD measurements for quantitative studies of microbial growth, including growth rates, lag times and cell yields, have thus far not been established.The Beer-Lambert law (Supplementary Note 1) assumes that light is only absorbed to derive OD ~ C, which is true if the light received by the detector of a typical spectrophotometer is the light that did not interact with the sample in any way 7,9 . In general, when microbial cells are well dispersed in the solution (for the cases where N is small, i.e. single scattering regime) and the geometry of the spectrophotometer is suitable, the Beer-Lambert law is a good approximation for turbidity measurements, and N (or C) is ~...

Biofuel alcohols have severe consequences on the microbial hosts used in their biosynthesis, which limits the productivity of the bioconversion. The cell envelope is one of the most strongly affected structures, in particular, as the external concentration of biofuels rises during biosynthesis. Damage to the cell envelope can have severe consequences, such as impairment of transport into and out of the cell; however the nature of butanol-induced envelope damage has not been well characterized. In the present study, the effects of nbutanol on the cell envelope of Escherichia coli were investigated. Using enzyme and fluorescence-based assays, we observed that 1% v/v n-butanol resulted in release of lipopolysaccharides from the outer membrane of E. coli and caused 'leakiness' in both outer and inner membranes. Higher concentrations of n-butanol, within the range of 2% -10% (v/v), resulted in inner membrane protrusion through the peptidoglycan observed by characteristic blebs. The findings suggest that strategies for rational engineering of butanoltolerant bacterial strains should take into account all components of the cell envelope.