Technical upgrade of an open-source liquid handler to support bacterial colony screening.

The optimization of genetically engineered biological constructs is a key step to deliver high-impact biotechnological applications. The use of high-throughput DNA assembly methods allows the construction of enough genotypic variants to successfully cover the target design space. This, however, entails extra workload for researchers during the screening stage of candidate variants.

An automated DIY framework for experimental evolution of Pseudomonas putida.

Adaptive laboratory evolution (ALE) is a general and effective strategy for optimizing the design of engineered genetic circuits and upgrading metabolic phenotypes. However, the specific characteristics of each microorganism typically ask for exclusive conditions that need to be adjusted to the biological chassis at stake. In this work, we have adopted a do-it-yourself (DIY) approach to implement a flexible and automated framework for performing ALE experiments with the environmental bacterium and metabolic engineering platform Pseudomonas putida.

Quantitative assessment of morphological traits of planktonic bacterial aggregates.

The efficiency of multi-strain planktonic flocs of bacteria as biocatalytic agents in aqueous media depends to a considerable extent on their three-dimensional aggregation patterns. Yet, numerical methodologies for full characterization of such heterogeneous biomass structures are largely missing. In this work we present a descriptive methodology for quantitatively portraying and identifying suspended cell clumps formed by planktonic bacteria.

Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies.

Background: Currently the combination of molecular tools, imaging techniques and analysis software offer the possibility of studying gene activity through the use of fluorescent reporters and infer its distribution within complex biological three-dimensional structures. For example, the use of Confocal Scanning Laser Microscopy (CSLM) is a regularly-used approach to visually inspect the spatial distribution of a fluorescent signal. Although a plethora of generalist imaging software is available to analyze experimental pictures, the development of tailor-made software for every specific problem is still the most straightforward approach to perform the best possible image analysis.

Assembly of a Custom-made Device to Study SpreadingPatterns of Biofilms.

Biofilms are bacterial communities in the shape of exopolysaccharide matrix-encased aggregates attached onto interphases able to resist environmental aggressions. The development of bacteria in the shape of biofilms deeply affects the performance of many industrial processes which work with fluidic systems, where bacteria may settle and prosper. As a consequence industrial equipment experiments low performance issues and substantial maintenance costs.

Dynamics of Pseudomonas putida biofilms in an upscale experimental framework.

Exploitation of biofilms for industrial processes requires them to adopt suitable physical structures for rendering them efficient and predictable. While hydrodynamics could be used to control material features of biofilms of the platform strain Pseudomonas putida KT2440 there is a dearth of experimental data on surface-associated growth behavior in such settings. Millimeter scale biofilm patterns formed by its parental strain P.

Physical Forces Shape Group Identity of Swimming Cells.

The often striking macroscopic patterns developed by motile bacterial populations on agar plates are a consequence of the environmental conditions where the cells grow and spread. Parameters such as medium stiffness and nutrient concentration have been reported to alter cell swimming behavior, while mutual interactions among populations shape collective patterns. One commonly observed occurrence is the mutual inhibition of clonal bacteria when moving toward each other, which results in a distinct halt at a finite distance on the agar matrix before having direct contact.

Stenosis triggers spread of helical Pseudomonas biofilms in cylindrical flow systems.

Biofilms are multicellular bacterial structures that adhere to surfaces and often endow the bacterial population with tolerance to antibiotics and other environmental insults. Biofilms frequently colonize the tubing of medical devices through mechanisms that are poorly understood. Here we studied the helicoidal spread of Pseudomonas putida biofilms through cylindrical conduits of varied diameters in slow laminar flow regimes.