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

<h4>Premise</h4>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.<h4>Methods</h4>We utilized population genomic data of the liverwort <i>Calasterella californica</i> obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space.<h4>Results</h4>The bacterial communities associated with <i>C. californica</i> were dominated by the methanotroph <i>Methylobacterium</i> 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.<h4>Discussion</h4>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.