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

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.

Ecological significance of Candidatus ARS69 and Gemmatimonadota in the Arctic glacier foreland ecosystems

“…Though several studies reported diversity and succession of microbial communities across the different GF ecosystems (Kim et al 2017 ; Schuette et al 2010 ; Schütte et al 2009 ; Venkatachalam et al 2021 ), only a few studies investigated functions and processes associated with microbial communities (Nash et al 2018 ; Varliero et al 2021 ). In particular, reconstructing MAGs directly from soil samples provides unique opportunities to study individual community members, their metabolisms, and their survival strategies (Maggiori et al 2021 ). In particular, the samples collected from the extreme environmental region are often much more difficult to cultivate in the laboratory in comparison to other tropical regions.…”

Breaking the Ice: A Review of Phages in Polar Ecosystems

“…The sediment and meltwater above remain in approximate equilibrium of the glacier surface, usually tens of centimeters below the surface [162,145]. Despite their small size and dynamic conditions, cryoconite holes host actively growing microbial communities [163], and the viruses that parasitize them [148,164]. Although viral production rates in Arctic cryoconite holes have been measured as similar to other sediments around the globe, microscopy-suggested burst sizes were substantially lower (only 2-4 viruses cell -1 ).…”

Hybrid Assembly Improves Genome Quality and Completeness of Trametes villosa CCMB561 and Reveals a Huge Potential for Lignocellulose Breakdown

“…Furthermore, based on the BUSCO analysis (Figure 1c), the newly assembled genome has better completeness indices and fewer duplicated, fragmented, and missing genes. Similarly, Maggiori et al (2021) demonstrated that by using a hybrid assembly approach (HiSeq + MinION), it was possible to obtain a greater number of genomes from metagenomic samples, with longer contigs, more coding sequences, higher completeness, less contamination, and higher N50 [66].…”