Metabarcoding from Microbes to Mammals: Comprehensive Bioassessment on a Global Scale

The rise in DNA metabarcoding can be seen by the exponential increase in the number of publications using this approach for bioassessment. However, most metabarcoding studies are limited to a modest scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. Illumina’s MiSeq is currently the most common sequencing platform used for these metabarcoding applications. With the advent of next-next-generation, deep-sequencing platforms (e.g., Illumina NovaSeq), comprehensive bioassessment of all the organisms in a sample is possible. Technological advancements, including enhanced instrument sensitivity of deep-sequencing platforms, usher in exciting possibilities to obtain more information from sequenced DNA. Here, we present a case study comparing the capacity of NovaSeq to provide high-resolution taxonomic recovery compared to the incumbent MiSeq platform. We then explore the added value that ultra-deep sequencing affords, including possibilities for merging whole-system DNA metabarcoding with occupancy modeling, phylogentics, population genetics, functional gene analysis, and ecological network analysis. We conclude by discussing barriers to these advancements, highlighting the need for (1) standardized sampling protocols for environmental genomics sampling that will enable networks of scientists—and citizen scientists—to scale up sample collection to global scales, (2) experts and computational resources to handle the deluge of genomic data, (3) standardized, open-source bioinformatic pipelines, and (4) genomics centres to handle the sequencing capacity required to generate comprehensive, near real-time biodiversity information. Each of these challenges will need to be overcome to address the global biodiversity crisis we now face.