Off-target metagenomics: Leveraging whole genomesequencing to study the bacteriome of the liverwortCalasterella californica

Abstract

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSPremise of studyC_ST_ABSThe 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 pipelines and databases enable the use short reads to study bacterial communities associated with organisms. MethodsWe 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. Key resultsThe 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 was 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. ConclusionsOur 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. Our novel off-target metagenomics approach can be applied to any population level re-sequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using re-purposed data from landscape genomics.