UNLOCK

The facility

UNLOCK is a unique large-scale research infrastructure that facilitates research on mixed microbial communities. It consists of three experimental platforms (Biodiscovery, Modular Bioreactor, Parallel Cultivation) and a FAIR data platform. UNLOCK provides a wide range of users with easily accessible and affordable state-of-the-art facilities and equipment, which allow for research resulting in scientific discovery and practical applications. Facilities are equipped to work with strictly anaerobic microorganisms. 

Research topics

Mixed microbial communities, biodiscovery, bioreactor, cultivation, defined communities, biorecovery, water reuse, waste streams, microbial community development, FAIR data. 

References

Kleerebezem, R., Stouten, G., Koehorst, J., Langenhoff, A., Schaap, P., & Smidt, H. (2021). Experimental infrastructure requirements for quantitative research on microbial communities. Current Opinion in Biotechnology, 67, 158-165. https://doi.org/10.1016/j.copbio.2021.01.017  

Poncheewin,  W., van Diepeningen, A. D., van der Lee, T. A. J., Suarez-Diez, M., & Schaap, P. J. (2022). Classification of the plant-associated lifestyle of Pseudomonas strains using genome properties and machine learning. Scientific Reports, 12, 10857. https://doi.org/10.1038/s41598-022-14913-4  

Atasoy, M., Scott, W. T. Jr., van Gijn, K., Koehorst, J. J., Smidt, H., & Langenhoff, A. A. M. (2023). Microbial dynamics and bioreactor performance are interlinked with organic matter removal from wastewater treatment plant effluent. Bioresource Technology, 372, 128659. https://doi.org/10.1016/j.biortech.2023.128659  

For a full overview of publications, see: https://m-unlock.com/publications/.  

Running period

2020-2030 (and beyond) 

Equipment

UNLOCK consists of four platforms, each with their own facilities: 

Biodiscovery Platform 

• Microbioreactor unit for the initial screening of mixed microbial communities. 
• High throughput sample processing unit for simultaneous extraction and analysis of biomolecular fractions from single samples. 
• Raman assisted microfluidic cell sorting unit to sort and characterise cells form a targeted population of interest for downstream cultivation. 
• MicroWriter ML3 Pro: an advanced benchtop photolitography system, to generate microfluidic chips. 
• Oxford Nanopore Technology (ONT) Sequencing, through two devices: 
• GridION, for whole genome analysis, metagenomics, targeted sequencing, and large and small transcriptomes. 
• PromethION 2 Solo, for whole mammalian genome sequencing, complete metagenomes, large targeted sequencing, and RNA sequencing applications. 

FAIR Data Platform 

• iRODS: open source data management system to manage operational (meta)data of UNLOCK experiments. 
• FAIR data station: simple metadata registration tool for experimentalists/data producers. 
• Kubernetes Cluster 
• Modelling tools to simulate microbial community behaviour. 
• Multiple workflows, including metagenomic binning, various RNAseq workflows, and quality control. 

Modular Bioreactor Platform 

• Standard bioreactors (8 units). 
• Bio-electrochemical systems (BES, 4 units). 
• High pressure & high temperature reactors (4 units). 
• Outdoor constructed wetlands (CW, 3 units of 12 m3) directly fed with municipal wastewater. 
• Mass Spectrometer (MS) for continuous and automated monitoring of bioreactor and bio-electrochemical gas production. 
• Online liquid with a Nuclear Magnetic Resonance (NMR) spectroscopy to monitor molecules with an atomics level precision. 
• Various sensors (Raman spectrometer, ultraviolet (UV) sensor, pH, Oxidation-Reduction (ORP) sensor, biomass sensor) for in-line liquid analyses. 
• High-pressure liquid chromatography, gas chromatography, ion chromatography for offline liquid and gas analyses. 
• TRACE C2 sampling tool, for automated sampling at preset intervals. 
• GX-271 Gilson liquid handler: medium capacity liquid handler and autosampler. 

Parallel Cultivation Platform 

• Standard experimental set-up (30 units), meant for low-maintenance long-term (1-12 months) experiments on the functional development of microbial communities. Includes: 
• 0.5-2.0 liter bioreactors, can be operated as sequencing batch reactor (SBR), chemostat, retentostat, and other dynamic feeding profiles. 
• Full automated control system to define & control substrate supply patterns and environmental conditions. 
• On-line MS based off gas composition and flow measurement. 
• Intensive experimental set-up (10 units), meant for short-term experiments (1-10 weeks) on the effect of a specific process on the functional and molecular development of a specific microbial community. Includes: 
• Ultrafiltration sampling unit. 
• Liquid samples for off-line analysis. 
• Equipment available: 
• Bioreactors 
• Mass spectrometer 
• Pumps  
• Utilities 
• Biocontrollers 

Data management

UNLOCK supports FAIR data collection and data management through its own FAIR Data Station. With the FAIR Data Station, users select which metadata standard they would like to use. The data producers provide metadata according to the chosen standards, after which the system checks the metadata for completeness and correctness. The metadata are transformed into a machine-actionable FAIR resource. More information can be found here.  

Available datasets

Not applicable at this point. All data generated at UNLOCK, excluding data from commercial projects, adheres to open science standards and is made publicly available. 

Conditions for access

Researchers from both academic and commercial organisations can submit a proposal for a project, which will be evaluated by an evaluation committee, who will assess the proposal and provide feedback within a month. The full application process can be found here.  

The four different platforms charge different fees per day/month of use. The fees for academic users are heavily subsidised. For an overview of costs and services included, see this webpage.