Pangenomes reveal genomic signatures of microbial adaptation to experimental soil warming

Abstract

Evolutionary responses to anthropogenic climate change are irreversible and largely uncaptured by climate models. Below-ground carbon trans- formations represent an important natural mitigation solution, but novel adaptive traits may alter microbial climate feedback mecha- nisms. To better define microbial evolutionary responses to warming, we study microorganisms from an ongoing in situ soil warming exper- iment 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 lin- eages reflect adaptations related to growth and carbon utilization. From our culture collection of soil bacteria isolated from experimental heated and control plots, we sequenced genomes representing taxa dominant in soil communities and sensitive to warming, including independent lineages of Alphaproteobacteria, Actinobacteria, and Betaproteobac- teria. We investigated differences in genomic attributes and patterns of functional gene content to identify genetic signatures of adap- tation. Comparative pangenomics revealed differently abundant gene clusters with functional annotations related to carbon and nitrogen metabolism. We also observe differences in genome-wide codon usage bias between heated and control genomes, suggesting potential adaptive traits related to growth or growth efficiency. Together, these data illus- trate the emergence of diverse lineage-specific adaptive traits as well as common ecological-evolutionary microbial responses to climate change.

Thermal adaptation of soil microbial growth traits in response to chronic warming

“…The long fragment buffer provided in the sequencing kit was used in an extended 10 min incubation at 37℃ to enrich for high-molecular weight DNA. The flow cell was primed using the Flow Cell Priming Kit (Oxford Nanopore Technologies), and 15 fmol of the library was mixed with the sequencing buffer and loading beads and then loaded through the Spot-On port of the flow cell ( 24 ).…”

Thermal adaptation of soil microbial growth traits in response to chronic warming

“…The long fragment buffer provided in the sequencing kit was used in an extended 10 minute incubation at 37℃ to enrich for high-molecular weight DNA. The flow cell was primed using the Flow Cell Priming Kit (Oxford Nanopore Technologies, UK), and about 15 fmols of the library was mixed with the sequencing buffer and loading beads and then loaded through the Spot-On port of the flow cell (Choudoir et al, 2023).…”