Acclimation and Adaptation in Soil Microbes After 23 years of Warming

Microbes have crucial functions in natural and managed soil ecosystems - they break down plant material, release inorganic nutrients that stimulate plant growth, promote soil aggregation and, after death, contribute to long-term stable soil organic matter, thereby improving plant health and productivity, increasing soil water holding capacity, and reducing wind and water erosion. Although laboratory experiments have revealed a broad range of mechanisms that microbes use to adapt to environmental variation – from physiological adjustments to genetic changes – it has been challenging to study microbes in their natural environment. Such an analysis has now become possible after advances in DNA and RNA sequencing technologies. This project will analyze how microbial organisms in four grassland ecosystems, spanning temperate to semi-arid regions, have adapted to 23 years of temperature increase. Researchers will also determine whether 23 years of warming has resulted in altered plant-soil-microbe interactions and plant growth. Finally, this project will study changes in gene expression and genetic and genomic changes in microbial organisms under high resource availability where strong selection pressure selects for microbial traits that result in faster and more efficient growth. By improving our understanding of microbial adaptation to environmental stressors, this project contributes to new approaches to improve soil and plant health in natural and managed ecosystems. This project will provide research opportunities for one postdoctoral researcher, two PhD students, and several undergraduate students. This study will analyze how gene-expression and genetic and genomic traits of individual microbial species have changed in response to 23 years of elevated temperature in a meadow in a mixed conifer and a ponderosa pine forest, grassy interspaces in a Pinion-Juniper woodland, and a cool desert grassland ecosystem after transplanting whole plant-soil mesocosms at their own and lower (warmer) elevation. Analysis of transcription will focus on biosynthesis of amino acids, lipids, nucleotides, cell wall, EPS, and biofilm, energy production, central C metabolic network processes, stress responses, regulation, and secondary metabolism. MAGs will be assembled using long-read sequencing and genomes of closely related taxa in warmed and control soil will be compared. Finally, taxon-specific growth rates will be measured using quantitative stable isotope probing with 18O-labeled water in bulk and exudate-amended soil. Three experiments are planned: (1) a comparison of growth rate, gene-expression, and genetic and genomic traits for control and transplanted soil communities after 23 years, (2) a study of plant-soil-microbiome interactions after 23-years of elevated temperature using greenhouse and field experiments, and (3) an investigation of the mechanisms of adaptation under two temperatures and N treatments in Adaptive Laboratory Evolution experiments. This work will inform theoretical questions in microbial eco-evolution, such as, among others, the existence of growth rate and biomass yield trade-offs, the role of resource availability in genome streamlining, and predator-prey coevolution. This research advances knowledge of microbial evolution in complex communities and may result in practical applications in restoration ecology, bioremediation, agriculture, and human health. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.