MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes

• Published in: Scientific Reports
• Main Authors: Catherine Maggiori, Isabelle Raymond-Bouchard, Laura Brennan, David Touchette, Lyle Whyte
• Format: Article in Journal/Newspaper
• Language: English
• Published: Nature Portfolio 2021
• Subjects: Medicine; R; Science; Q; Nunavut; Allen Bay; Sea ice
• Online Access: https://doi.org/10.1038/s41598-021-00026-x; https://doaj.org/article/20d5c449149f44be90866e45fe586d26

Abstract Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites—HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)—where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus’s only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment.