Comparison of in-field Nanopore sequencing with laboratory based Illumina sequencing of shotgun metagenomes

In the field of observation, chance favours only the prepared mind (Pasteur). Impressive developments in genomics have led microbiology to its third “Golden Age”. However, conventional metagenomics strategies necessitate retrograde transfer of samples from extreme or remote environments for later analysis, rendering the powerful insights gained retrospective in nature, striking a contrast with Pasteur's dictum. Here we implement highly portable USB-based Nanopore DNA sequencing platforms coupled with field-adapted environmental DNA extraction, rapid sequence library generation and off-line analyses of shotgun metagenome and 16S ribosomal RNA gene amplicon profiles to characterize microbiota dwelling within cryoconite holes upon Svalbard glaciers, the Greenland Ice Sheet and the European Alps. In-field Nanopore sequencing of metagenomes captures taxonomic composition of supraglacial microbiota, while 16S rRNA gene amplicon sequencing resolves bacterial community responses to habitat changes. We benchmark the capability of in-field microbiome sequencing to characterize microbial communities by comparison of Nanopore data with public Illumina metagenomic data and 16S rRNA gene V1-V3 pyrosequencing from the same samples, demonstrating a high level of coherence between profiles obtained from Nanopore sequencing and laboratory based sequencing approaches. Ultimately, in-field sequencing potentiated by Nanopore devices raises the prospect of considerably enhanced agility in exploring Earth's microbiomes.