Abstract

Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenomic sequencing. For reliable monitoring of AD via long reads, we established a robust protocol for obtaining less fragmented, high-quality DNA, while preserving bacteria and archaea composition, for a broad range of different biogas reactors. Samples from 20 different biogas/wastewater reactors were investigated, and a median of 20.5 Gb sequencing data per nanopore flow cell was retrieved for each reactor using the developed DNA isolation protocol. The nanopore sequencing data were compared against Illumina sequencing data while using different taxonomic indices for read classifications. The Genome Taxonomy Database (GTDB) index allowed sufficient characterisation of the abundance of bacteria and archaea in biogas reactors with a dramatic improvement (1.8- to 13-fold increase) in taxonomic classification compared to the RefSeq index. Both technologies performed similarly in taxonomic read classification with a slight advantage for Illumina in regard to the total proportion of classified reads. However, nanopore sequencing data revealed a higher genus richness after classification. Metagenomic read classification via nanopore provides a promising approach to monitor the abundance of taxa present in a microbial AD community as an alternative to 16S ribosomal RNA studies or Illumina Sequencing.

Keywords

nanopore; sequencing; DNA extraction; metagenome; abundance; GTDB; nanopore

Published in

Applied Sciences
2020, Volume: 10, number: 21, article number: 7518
Publisher: MDPI

SLU Authors

• Brandt, Christian

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

• Bongcam Rudloff, Erik

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

• Müller, Bettina

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

Sustainable Development Goals

Ensure access to affordable, reliable, sustainable and modern energy for all


UKÄ Subject classification

Bioinformatics (Computational Biology)


Publication identifier

DOI: https://doi.org/10.3390/app10217518

Permanent link to this page (URI)

https://res.slu.se/id/publ/109360