Pangenomes reveal genomic signatures of microbial adaptation to experimental soil warming

Abstract

Below-ground carbon transformations represent a natural climate change mitigation solution, but newly-acquired traits adaptive to climate stress may alter microbial climate feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment at the Harvard Forest Long-term Ecological Research (LTER) site where, for over three decades, soils are continuously heated 5 °C above ambient temperatures. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect trait-based adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing taxa dominant in soil communities and sensitive to warming, including lineages of Alphaproteobacteria, Actinobacteria, and Betaproteobacteria. We investigated differences in genomic attributes and patterns of functional gene content to identify genomic signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation. Overall, genomes from control plots were relatively enriched in carbon and fatty acid metabolism pathways, while genomes from heated plots were relatively enriched in nitrogen metabolism pathways. We also observed differences in global codon usage bias between heated and control genomes, suggesting potential adaptive traits related to growth or growth efficiency. This effect was more varied for organisms with fewer 16S rrn operons, suggesting that these organisms experience different selective pressures on growth efficiency. Together, these data illustrate the emergence of lineage-specific traits as well as common ecological-evolutionary microbial responses to climate change.