Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient

Abstract

Microbial community responses to environmental change are largely associated with ecological processes; however, the potential for microbes to rapidly evolve and adapt remains relatively unexplored in natural environments. To assess how ecological and evolutionary processes simultaneously alter the genetic diversity of a microbiome, we conducted two concurrent experiments in the leaf litter layer of soil over 18 mo across a climate gradient in Southern California. In the first experiment, we reciprocally transplanted microbial communities from five sites to test whether ecological shifts in ecotypes of the abundant bacterium, Curtobacterium, corresponded to past adaptive differentiation. In the transplanted communities, ecotypes converged toward that of the native communities growing on a common litter substrate. Moreover, these shifts were correlated with community-weighted mean trait values of the Curtobacterium ecotypes, indicating that some of the trait variation among ecotypes could be explained by local adaptation to climate conditions. In the second experiment, we transplanted an isogenic Curtobacterium strain and tracked genomic mutations associated with the sites across the same climate gradient. Using a combination of genomic and metagenomic approaches, we identified a variety of nonrandom, parallel mutations associated with transplantation, including mutations in genes related to nutrient acquisition, stress response, and exopolysaccharide production. Together, the field experiments demonstrate how both demographic shifts of previously adapted ecotypes and contemporary evolution can alter the diversity of a soil microbiome on the same timescale.

Keywords: Curtobacterium; adaptation; ecotypes; experimental evolution; reciprocal transplant.

Fig. 1.

Microbial community transplant experiment. (A) Changes in microbial community composition can be due to a continuum of ecological and evolutionary processes. For instance, shifts in standing genetic variation can be attributed to both ecological and evolutionary processes depending on the level of biological resolution, while de novo mutations can be a result from evolutionary adaptation. (B) A schematic of the two parallel transplant experiments at the community and strain level. Inoculated litterbags were transplanted to all sites along an elevation gradient that covaried in temperature and precipitation. Site codes: D=Desert; Sc=Scrubland; G=Grassland; P=Pine-Oak; S=Subalpine.

Fig. 2.

The composition of Curtobacterium diversity along the climate gradient after 18 mo of transplant. Principal Component Analysis (PCA) ordination plot depicting Curtobacterium composition in each metagenomic sample, colored by site with shapes representing inoculum. PC1 explains the largest amount of variation, which is driven by differences in absolute Curtobacterium abundances in the samples (SI Appendix, Fig. S2B). The ellipses are 75% CIs around the inoculum samples that remained in their native site (e.g., the red ellipse represents the spread of the red triangles, and the purple ellipse represents the spread of the purple diamonds). The vectors represent the contribution of the top six abundant ecotypes to compositional differences along the two axes.

Fig. 3.

Correlation of Curtobacterium functional traits to field sites. (A) CWM values for Curtobacterium ecotypes’ traits along a climate gradient for survey (surrounding leaf litter outside the litterbags) and after 18 mo of transplant to the sites denoted on the x-axis. Smoothed averages (lines) were calculated from locally weighted smoothing with CIs (colored areas). (B) A heatmap showing normalized production of biofilms, growth measurements (μ_max = maximum growth rate; A_max = maximum growth [OD₆₀₀]), degradation for cellulose and xylan, and optimal temperature across all assays between the top six abundant Curtobacterium ecotypes. Phylogeny derived from multilocus alignment of Curtobacterium core genes.

Fig. 4.

Mutation distribution across a Curtobacterium ancestral strain after transplant across the elevation gradient. (A) Mutations in 112 evolved clones isolated from five sites along the climate gradient at 6 (Time point 1), 12 (T2), and 18 mo (T3) intervals. Includes 30 strains from the Desert (D) site, 22 at Scrubland (Sc), 11 at Grassland (G), 24 at Pine–Oak (P), and 25 at Subalpine (S). Nonrandom mutations also observed in the population data are denoted for synonymous (syn), nonsynonymous (nonsyn), and nonsense mutations. (B) The total number of mutations per mutant strain by time point and site. (C) Lack of evidence for positive selection in the evolved populations in the base substitutions of expected (from base change spectrum) and observed dN/dS ratios.