Combining and comparing meta-, mini meta-, and single-cell genomics to characterize a bacterial community in acidic agricultural soil
Agricultural soil acidification is an acknowledged consequence of intensive farming and is known to negatively impact crop yields as well as modify bacterial diversity and abundance. However, much is yet to be discovered regarding the potential functional shift of these microbes, their interactions, or simply their identification. The study of bacteria is highly dependent on molecular tools with specific technologies, scales, and interpretation boundaries. Single-cell omics are gaining interest in microbial ecology, assessing genetic diversity at the population and community level, and linking each cell to its functions. Here, we compare the use of metagenomic, mini-metagenomic, and single-cell genomic analyses on an identical bacterial community. The cells were extracted from a soil sample from the Craibstone experimental field, and genomes were sequenced following one of the three strategies. In doing so, we can identify and combine the strengths of each method to shed light on this poorly known kingdom.