On-site sequencing speeds up and re-directs field-based microbiology.

Abstract

As a field-going molecular microbial ecologist, I often experience an extreme high feeling or bout of excitement during immersion in my study environment. However, when I return to my laboratory, generally in the cold and dark winter months, I ‘crash’ or reach a low point, due to my realization of how many samples we obtained in the field and the extent of processing, sequencing and analysis time that we still need to devote to the samples before we can draw any conclusions and share our findings. In an effort to lessen my now regular post-field crashes, I have started following the development of mobile sequencing technology. Oxford Nanopore Technologies has recently made large strides in this area, producing the MinION a hand-held flow-cell costing $1,000 that can connect to a laptop computer. The company is developing the even more mobile SmidgION, a lower power device that will run on a smartphone. Depending on the type of MinION sequencing conducted (amplicon, metagenomic, transcriptomic, etc.), preparation after extraction of nucleic acids can take as little as 10-minutes to a few hours, and sequencing reads are immediately available for viewing during the sequencing run. While the platform has been primarily used for DNA molecules, the MinION can directly sequence RNA (without conversion to cDNA), opening up new avenues for exploring microbial transcripts as well as RNA viruses while on-site. Within environmental microbiology, this technology has recently been applied at field sites, including soils and remote glacier environments (Cummings et al., 2017; Edwards et al., 2018) and has also been used to track wastewater contamination from urban storm water (Hu et al., 2018). The ability to produce sequencing data while in the field could transform the timeline of many environmental microbiology-based studies...