Patterning of Microorganisms and Microparticles through Sequential Capillarity-assisted Assembly

Summary

We present a technology that uses capillarity-assisted assembly in a microfluidic platform to pattern micro-sized objects suspended in a liquid, such as bacteria and colloids, into prescribed arrays on a polydimethylsiloxane substrate.

Abstract

Controlled patterning of microorganisms into defined spatial arrangements offers unique possibilities for a broad range of biological applications, including studies of microbial physiology and interactions. At the simplest level, accurate spatial patterning of microorganisms would enable reliable, long-term imaging of large numbers of individual cells and transform the ability to quantitatively study distance-dependent microbe-microbe interactions. More uniquely, coupling accurate spatial patterning and full control over environmental conditions, as offered by microfluidic technology, would provide a powerful and versatile platform for single-cell studies in microbial ecology.

This paper presents a microfluidic platform to produce versatile and user-defined patterns of microorganisms within a microfluidic channel, allowing complete optical access for long-term, high-throughput monitoring. This new microfluidic technology is based on capillarity-assisted particle assembly and exploits the capillary forces arising from the controlled motion of an evaporating suspension inside a microfluidic channel to deposit individual microsized objects in an array of traps microfabricated onto a polydimethylsiloxane (PDMS) substrate. Sequential depositions generate the desired spatial layout of single or multiple types of micro-sized objects, dictated solely by the geometry of the traps and the filling sequence.

The platform has been calibrated using colloidal particles of different dimensions and materials: it has proven to be a powerful tool to generate diverse colloidal patterns and perform surface functionalization of trapped particles. Furthermore, the platform was tested on microbial cells, using Escherichia coli cells as a model bacterium. Thousands of individual cells were patterned on the surface, and their growth was monitored over time. In this platform, the coupling of single-cell deposition and microfluidic technology allows both geometric patterning of microorganisms and precise control of environmental conditions. It thus opens a window into the physiology of single microbes and the ecology of microbe-microbe interactions, as shown by preliminary experiments.

Introduction

Spatial patterning of single microorganisms, particularly within experimental arenas that enable full control over environmental conditions, such as microfluidic devices, is highly desirable in a broad range of contexts. For example, arranging microorganisms into regular arrays would permit the accurate imaging of large numbers of individual cells and the study of their growth, physiology, gene expression in response to environmental stimuli, and drug susceptibility. It would also allow studying cell-cell interactions of particular interest in research into cellular communication (e.g., quorum sensing), cross-feeding (e.g., algal-bacterial symbiosis), or antagoni....

Protocol

1. Silicon master preparation

NOTE: The PDMS templates bearing the microfabricated traps that form the template for colloidal and microbial patterning were fabricated according to the method introduced by Geissler et al.¹⁷. The silicon master was prepared by conventional lithography in a cleanroom. See the following steps for the procedure and the Table of Materials for the equipment.

1. Design the features using computer-aided design (CAD) software.
2. Prepare the chrome-glass mask with a layer of positive photoresist by exposing the designed featur....

Results

A microfluidic platform that exploits capillarity-assisted assembly to pattern colloidal particles and bacteria into traps microfabricated on a PDMS template was developed. Two different channel geometries have been designed to optimize the patterning of colloids and bacteria through the capillarity-assisted assembly. The first channel geometry (Figure 1B) consists of three 23 mm long parallel sections with no physical barrier between them. The two sections on the sides are 5 mm wide and 1 m.......

Discussion

The microfluidic platform described here allows the patterning of micro-sized objects, such as colloids and bacteria, into prescribed spatial arrangements on a PDMS substrate. The full control over environmental conditions offered by microfluidics and the ability to pattern cells with micrometric precision granted by sCAPA technology makes it a very promising platform for future physiology and ecology studies.

In the experiments presented in this work, the silicon master was realized using the.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Alcatel AMS 200SE I-Speeder	Alcatel Micro Machining System		deep reactive ion exchange system
Alconox			detergent
AZ400K developer	MicroChemicals	AZ400K
BD 10 mL Syringe (Luer-Lock)	BD	300912	used to flush fresh Lysogeny broth into the microfluidic channel
Box Incubator	Life Imaging Services		used to ensure a uniform and constant temperature in the channel
Centrifuge	Eppendorf	5424R	used to replace the overnight media with fresh minimal media
Centrifuge vial	Eppendorf	30120086	1.5 mL
CETONI Base 120	CETONI GmbH		syringe pump
Fluorescent PS particles of diameter 0.98 µm (red)	microParticles GmbH	PS-FluoRed-Fi267
Fluorescent PS particles of diameter 1.08 µm (green)	microParticles GmbH	PS-FluoGreen-Fi182
Fluorescent PS particles of diameter 2.07 µm (green)	microParticles GmbH	PS-FluoGreen-Fi183
Fluorescent PS particles of diameter 2.08 µm (red)	microParticles GmbH	PS-FluoRed-Fi180
Gigabatch 310 M	PVA TePla		used to plasma treat a 10 cm silicon wafer
H401-T-CONTROLLER	Okolab		controller of the heated glass plate
H601-NIKON-TS2R-GLASS	Okolab		heated glass plate
Heidelberg DWL 2000	Heidelberg Instruments		UV direct laser writer
Insulin syringes, U 100, with luer	Codan Medical ApS	CODA621640	1 mL syringe used to withdraw the liquid suspension during the patterning process
Klayout	Opensource		used to design the features on the silicon master
LB Broth, Miller (Luria-Bertani)	Fisher Scientific	244610	Lysogeny broth flushed into the microfluidic channel
Masterflex transfer tubing	Masterflex	HV-06419-05	0.020'' ID, 0.06'' OD
MOPS (10x)	Teknova	M2101	diluted tenfold with milliQ water and used to replace the overnight medium
Nikon Eclipse Ti2	Nikon Instruments		microscope
openSCAD	Opensource		used to design the mold
OPTIspin SB20	ATM group	51-0002-01-00	spin developer
Plasma chamber Zepto	Diener Electronic	ZEPTO-1	used to plasma treat the template and microchannel to bond them
Positive photoresist AZ1505	MicroChemicals	AZ1505
Potassium phosphate dibasic	Sigma Aldrich	P3786	added to MOPS 1x
Prusa curing and Washing machine CW1S	Prusa		used to ensure all polymer is cured and uncured polymer is removed from the mold
Prusa Resin - Tough	Prusa Research a.s.		UV photosensitive 405nm liquid resin for 3D printing
Prusa SL1 3d printer	Prusa		used to print the mold
Scale	VWR-CH	611-2605	used to weight PDMS mixture
Silicon wafer (10 cm)	Silicon Materials Inc.		N/Phos <100> 1-10 Ω cm
Süss MA6 Mask aligner	SUSS MicroTec Group		used to align the chrome-glass mask and the substrate, and expose the substrate
Sylgard 184	Dow Corning		silicone elastomer kit; curing agent
Techni Etch Cr01	Technic		chromium etchant
Trichloro (1H, 1H, 2H, 2H-perfluorooctyl) silane	Sigma Aldrich	448931	used to silianize the 3D printed mold
TWEEN 20	Sigma Aldrich	P1379	used to ensure an optimal receding contact angle during the patterning process
Veeco Dektak 6 M	Veeco		profilometer
VTC-100 Vacuum Spin Coater	MTI corporation		vacuum spin coater