Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere

Abstract

In environmental metagenomic experiments, a very high proportion of the microbial sequencing data (> 70%) remains largely unexploited because rare and closely related genomes are missed in short-read assemblies. The identity and the potential metabolisms of a large fraction of natural microbial communities thus remain inaccessible to researchers. The purpose of this study was to explore the genomic content of unassembled metagenomic data and test their level of novelty. We used data from a three-year microbial metagenomic time series of the NW Mediterranean Sea, and conducted reference-free and database-guided analysis. The results revealed a significant genomic difference between the assembled and unassembled reads. The unassembled reads had a lower mean identity against public databases, and fewer metabolic pathways could be reconstructed. In addition, the unassembled fraction presented a clear temporal pattern, unlike the assembled ones, and a specific community composition that was similar to the rare communities defined by metabarcoding using the 16S rRNA gene. The rare gene pool was characterised by keystone bacterial taxa, and the presence of viruses, suggesting that viral lysis could maintain some taxa in a state of rarity. Our study demonstrates that unassembled metagenomic data can provide important information on the structure and functioning of microbial communities.

Microbial Response to Natural Disturbances: Rare Biosphere often plays a role

“…Rare taxa have been defined based on several different approaches. For instance, Debroas et al defined rare biosphere as unassembled reads with low sequence depth coverage, without obtaining population genomes, and bioinformatically annotated those unassembled reads by mapping them to pre-annotated databases in order to infer functions carried by the rare taxa [72]. However, this approach cannot link these functions with specific taxa and derive species abundance dynamics since these unassembled short reads are typically not linked to each other and/or a phylogenetic marker.…”

Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus–host pairing of freshwater bacteria

“…S6). Their metagenomic detection indicates their presence in the samples, although they were unassembled in the metagenomes, presumably due to their low abundance or high genomic microdiversity, which hinders metagenomic assembly (47)(48)(49). By contrast, SAG-derived viruses not detected by metagenomic read mapping indicate their absence in the metagenomic samples, possibly because of the temporal shift of the viral community in the lake, as the metagenomes were collected 3-4 years prior to the collection of our SAGs.…”