OmiBox performance in the field
The aim of this project was to design and develop a portable (yet fully equipped) field laboratory that is autonomously operated at any sampling area targeted, regardless its remoteness.
Design and initial performance tests
The first step was to design, adapt and assemble all the necessary equipment and electrical systems that conform OmiBox. This was initially done in our in-house laboratories at Umeå University (Department of Ecology and Environmental Sciences).
Assessing sample processing workflow
Once the structure and power systems were properly implemented, the next step was to optimise laboratory workflows for efficient metagenomic and metatranscriptomic analyses. Sample processing times and library preparation steps were optimised to reduce the time and resources needed to go from a raw environmental sample to a genomic library ready to be sequenced.
Deploying OmiBox in the field
In order to shelter OmiBox from potentially rough environmental conditions, we use a large base camp tent that can be easily set up next to the sampling area. Next, OmiBox was brought inside and deployed. All the necessary equipment (isolator, MinION sequencers, homogeniser, Qubit fluorometer, etc.) is accommodated inside OmiBox in difference hard cases. Portable solar panels are set up alongside the tent and connected to OmiBox power station, which can then run all the equipment entirely by solar power.
Sample collection and processing
Our sampling area was located near by Umeå Maine Sciences Centre (Norrbyn, Sweden). Since it was early April, this coastal area was still partially covered by an ice layer, so we used an hovercraft to access a proper sampling spot. By an ice driller, we pierce through the ice and used a core sampler to collect sediment cores.
Thereafter, we retuned to our base camp where Omibox was deployed, which was near the sampling area, next to the coastal line. We immediately collected sediment samples from the cores and started the sample processing right away, from DNA/RNA extraction to library preparation.
Nanopore sequencing
Once our libraries were finally ready, we proceeded to the final step: sequencing by our MinION Mk1C. This step basically consists on the preparation of the Nanopore flow cell, loading the genomic library into the flow cell, configuring the sequencing parameters and simply start the sequencing.
Once the sequencing was started, we wrapped up our equipment, OmiBox, and the camp tent. After cleaning up the camping area, we returned to our in-house laboratories at Umeå University, where MinION Mk1C continued the sequencing for about 32 hours. This was possible by connecting the MinION to our portable power station, so that the sequencing can continue either in the field or anywhere else.