Single-cell variability of growth interactions within a two-species bacterial community

Tracking the stochastic growth of bacterial populations in microfluidic droplets

Bacterial growth in microfluidic droplets is relevant in biotechnology, in microbial ecology, and in understanding stochastic population dynamics in small populations. However, it has proved challenging to automate measurement of absolute bacterial numbers within droplets, forcing the use of proxy measures for population size. Here we present a microfluidic device and imaging protocol that allows high-resolution imaging of thousands of droplets, such that individual bacteria stay in the focal plane and can be counted automatically. Using this approach, we track the stochastic growth of hundreds of replicate Escherichia coli populations within droplets. {We find that, for early times, the statistics of the growth trajectories obey the predictions of the Bellman-Harris model, in which there is no inheritance of division time. Our approach should allow further testing of models for stochastic growth dynamics, as well as contributing to broader applications of droplet-based bacterial culture.

Coexistence of fluorescent Escherichia coli strains in millifluidic droplet reactors

Understanding competition and cooperation within microbiota is of high fundamental and clinical importance, helping to comprehend species' evolution and biodiversity. We co-encapsulated and cultured two isogenic Escherichia coli strains expressing blue (BFP) and yellow (YFP) fluorescent proteins into numerous emulsion droplets and quantified their growth by employing fluorescence measurements. To characterize and compare the bacterial growth kinetics and behavior in mono and co-culture, we compared the experimental observations with predictions from a simple growth model. Varying the initial ratio (R0) of both cell types injected, we observed a broad landscape from competition to cooperation between both strains in their confined microenvironments depending on start frequency: from a nearly symmetric situation at R0 = 1, up to the domination of one subpopulation when R0 ≫ 1 (or R0 ≪ 1). Due to competition between the strains, their doubling times and final biomass ratios (R1) continuously deviate from the monoculture behavior. The correlation map of the two strains' doubling times reveals that the R0 is one of the critical parameters affecting the competitive interaction between isogenic bacterial strains. Thanks to this strategy, different species of bacteria can be monitored simultaneously in real-time. Further advantages include high statistical output, unaffected bacteria growth, and long-time measurements in a well-mixed environment. We expect that the millifluidic droplet-based reactor can be utilized for practical clinical applications, such as bacterial antibiotic resistance and enzyme reaction kinetics studies.

Microfluidic and mathematical modeling of aquatic microbial communities

Aquatic microbial communities contribute fundamentally to biogeochemical transformations in natural ecosystems, and disruption of these communities can lead to ecological disasters such as harmful algal blooms. Microbial communities are highly dynamic, and their composition and function are tightly controlled by the biophysical (e.g., light, fluid flow, and temperature) and biochemical (e.g., chemical gradients and cell concentration) parameters of the surrounding environment. Due to the large number of environmental factors involved, a systematic understanding of the microbial community-environment interactions is lacking. In this article, we show that microfluidic platforms present a unique opportunity to recreate well-defined environmental factors in a laboratory setting in a high throughput way, enabling quantitative studies of microbial communities that are amenable to theoretical modeling. The focus of this article is on aquatic microbial communities, but the microfluidic and mathematical models discussed here can be readily applied to investigate other microbiomes.

Microfluidic cultivation and analysis tools for interaction studies of microbial co-cultures

Microbial consortia are fascinating yet barely understood biological systems with an elusive intrinsic complexity. Studying microbial consortia and the interactions of their members is of major importance for the understanding, engineering and control of synthetic and natural microbial consortia. Microfluidic cultivation and analysis devices are versatile tools for the study of microbial interactions at the single-cell level. While there is a vast amount of literature on microfluidics for the investigation of monocultures only few studies on co-cultures have been conducted in this context. Here we give an overview of different microfluidic single-cell cultivation tools for the analysis of microbial consortia with a focus on their physiology, growth dynamics and cellular interactions. Finally, central challenges and perspectives for the future application of microfluidic tools for microbial consortia investigations will be given.