Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding

Abstract

The diversity of soil bacteria was analyzed via metabarcoding and metagenomic approaches using DNA samples isolated from the biocrusts of 12 different Arctic and Antarctic sites. For the metabarcoding approach, the V3-4 region of the 16S rRNA was targeted. Our results showed that nearly all operational taxonomic units (OTUs = taxa) found in metabarcoding analyses were recovered in metagenomic analyses. In contrast, metagenomics identified a large number of additional OTUs absent in metabarcoding analyses. In addition, we found huge differences in the abundance of OTUs between the two methods. The reasons for these differences seem to be (1) the higher sequencing depth in metagenomics studies, which allows the detection of low-abundance community members in metagenomics, and (2) bias of primer pairs used to amplify the targeted sequence in metabarcoding, which can change the community composition dramatically even at the lower taxonomic levels. We strongly recommend using only metagenomic approaches when establishing the taxonomic profiles of whole biological communities.

Metagenomic Analysis of Antarctic Biocrusts Unveils a Rich Range of Cold-Shock Proteins

“…Furthermore, the dominant bacterial phylum in the Lang37 and Syo6 samples was cyanobacteria, which is consistent with the results of 16 S rRNA sequencing Contrary to the results of amplicon sequencing, the samples Amu8 and Amu14, analyzed by metagenomic sequencing, exhibited a dominance of actinobacteria, while Skar18 had a higher number of reads assigned to proteobacteria. Previous comparative analysis between these two sequencing techniques demonstrated that metagenomics is a more preferable tool for evaluating microbial community structure when compared to amplicon sequencing [15]. Only 4% of the assembled contigs was annotated to GO by EggNOG (Table 1).…”

Editorial: Polar Genomics in a Changing World

“…While technical advances are producing ever more robust insights into patterns of polar biodiversity, they can also sometimes bring into question inferences based on more classical approaches. For example, Becker and Pushkareva [21] compared the outcome of metabarcoding and metagenomic approaches applied to polar communities of soil bacteria. Using consistent bioinformatic workflows applied to the same samples, they found substantial differences in the inferred abundance of various taxa between the two methods, while metagenomics also identified a greater overall diversity of microbial taxa.…”

Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes

“…Investigating the relationship between MAGs and V9 OTUs is of further interest as there is an ongoing debate regarding which of the two approaches is more accurate in representing underlying biological entities [ 7 , 36 – 38 ]. Previous comparisons of metagenomics and metabarcoding data [ 23 , 39 , 40 ] have focused on selected groups for which high-quality reference sequences are available, whereas others compared only the diversity of higher-rank taxa, with no attempt to match individual MAGs to metabarcoding OTUs [ 41 ], or focused on prokaryotes [ 42 ].…”