Off-target metagenomics: Leveraging whole genome sequencing to study the bacteriome of the liverwort Calasterella californica

Abstract

Premise

The recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker-based pipelines enable the use of short reads to study bacterial communities associated with organisms.

Methods

We utilized population genomic data of the liverwort Calasterella californica obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space.

Results

The bacterial communities associated with C. californica were dominated by the methanotroph Methylobacterium and other Hyphomicrobiales, a group that includes well-known plant symbionts. While diversity metrics of bacteria composition were similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality.

Discussion

Our results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. The novel off-target metagenomics approach can be applied to any population-level resequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using repurposed data from landscape genomics.