Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

Abstract

We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology’s MinION portable sequencing platform, as well as summarize areas of recent development.

High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

“…Researchers usually have access to molecular laboratories that allow for more standardized and higher throughput sample processing than field-based assays. Yet, a minimalistic and mobile DNA barcoding system can be of great advantage when field sites are remote or hard to access, or when time is of the essence for swift generation of biodiversity information (reviewed in Krehenwinkel et al 2019b). Examples include monitoring of disease outbreaks (Quick et al 2016;Walter et al 2017) or documenting the immediate effects of ecological disasters such as forest fires or pipeline spillages.…”

Portable sequencing as a teaching tool in conservation and biodiversity research

“…In some cases, flowcells can be washed and reused within a few days with different barcodes to prevent cross-run sequence contamination. The development of many bioinformatic pipelines in recent years adds to the utility of DNA barcoding as a case study (see [6] for a review). Off-the-shelf software such as Geneious, UGene, or CLCGenomics are Graphical User Interface (GUI)-based but often pricier alternatives.…”

“…Other case studies include 16S metabarcoding of intestinal microbiota to assess gut health and diet or environmental DNA (eDNA) samples such as water and soil. Given the higher error rate of the MinION sequencer, scientific conclusions drawn from the data have to be treated carefully [6,20]. Nevertheless, we feel that these are valuable options for teaching.…”

“…Recent technological innovations, such as portable, low-cost instruments enabling nextgeneration sequencing in remote environments, are transforming this landscape [6]. A critical advancement is the development of Oxford Nanopore Technologies' (ONT's) MinION sequencing platform, which has many advantages compared to other HTS devices.…”

Analyzing the Dietary Diary of Bumble Bee

“…Since ITS2-amplicons generated with common primer pairs typically exceed the length of polymerase-derived NGS-reads, we are evaluating fulllength MinION-based ITS2-amplicon sequencing in contrast to NextSeq-based sequencing. From a technical perspective this work aims at developing field protocols for a rapid MinION-based assessment of pollen plant diversity in the field and utilization by pollinators, including estimation of crop pollination services delivered (Pomerantz et al, 2018;Krehenwinkel et al, 2019).…”