An open-source robotic platform that enables automated monitoring of replicate biofilm cultivations using optical coherence tomography

Luisa Gierl,Michael Wagner,Andrés Faíña,Harald Horn,Kasper Stoy

doi:10.1038/s41522-020-0129-y

Abstract

The paper introduces a fully automated cultivation and monitoring tool to study biofilm development in replicate experiments operated in parallel. To gain a fundamental understanding of the relation between cultivation conditions and biofilm characteristics (e.g., structural, mechanical) a monitoring setup allowing for the standardization of methods is required. Optical coherence tomography (OCT) is an imaging modality ideal for biofilms since it allows for the monitoring of structure in real time. By integrating an OCT device into the open-source robotic platform EvoBot, a fully automated monitoring platform for investigating biofilm development in several flow cells at once was realized. Different positioning scenarios were tested and revealed that the positioning accuracy is within the optical resolution of the OCT. On that account, a reliable and accurate monitoring of biofilm development by means of OCT has become possible. With this robotic platform, reproducible biofilm experiments including a statistical analysis are achievable with only a small investment of operator time. Furthermore, a number of structural parameters calculated within this study confirmed the necessity to perform replicate biofilm cultivations.

Highlights

Biofilms are microorganisms embedded in a matrix of extracellular polymeric substances[1]
It is required that the positioning accuracy is equal or smaller than the optical resolution of the Optical coherence tomography (OCT)
Due to the optical characteristics of the used GANYMEDE I OCT imaging system equipped with an LSM03/LK3 objective lens, the required positioning accuracy in the x- and y-direction needs to be ≤8 μm

Summary

Introduction

Biofilms are microorganisms embedded in a matrix of extracellular polymeric substances[1] They have several beneficial characteristics which today are of increasing interest, e.g. in cleaning up sewage or in producing platform chemicals, bioplastics or bioelectric currents. Lab-experiments often apply flow cell setups to improve our understanding of structure development and dynamics[4,5,6]; for example the effects of nutrient, substrate, and hydrodynamic conditions[7,8,9]. The determined population does not allow for a statistical analysis To tackle these challenges, combining a fast imaging modality to assess the biofilm structure with a positioning device allowing for the investigation/monitoring of several flow cells running in parallel would be preferable

Methods

Results

Conclusion