Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Impacts of Altered Climate on Microbial Growth and Nutrient Assimilation in an Ombitrophic Peat Bog


Sheryl L. Bell1*, Amy E. Zimmerman1, Bram W. G. Stone1, Kaitlin R. Rempfert1, Victoria Monsaint-Queeney2, Michaela Hayer2, Steven J. Blazewicz3, Kirsten S. Hofmockel1, and Bruce A. Hungate2


1Pacific Northwest National Laboratory; 2Northern Arizona University; and 3Lawrence Livermore National Laboratory


The work proposed here will integrate genomics- and isotope-enabled measurements of Growth Rate, growth Efficiency, and the stoichiometry of Essential Nutrients during growth, an integration researchers call GREEN omics. The overarching objective is to develop and apply omics approaches to investigate microbial community processes involved in nutrient cycling. The specific objectives of the proposed work are 1) to evaluate the microbial ecology of nutrient uptake, testing hypotheses about nutrient assimilation in response to temperature variation; 2) to evaluate the ecology of nutrient-use efficiency for soil microorganisms within a framework of ecological theory, and 3) to develop new isotope-enabled genomics and transcriptomics techniques that probe the microbial ecology of nutrient dissimilation. This work will push the frontier of isotope-enabled genomics by connecting quantitative stable-isotope probing to ecological theory about nutrient assimilation, nutrient-use efficiency, metabolic efficiency, and by applying these tools to understand the basic biology and ecology of soil microorganisms and how they transform nutrients in the environment.


Numerous studies have examined overall shifts in microbial community composition and diversity metrics under increased temperature, while far fewer have considered the importance of elevated CO2 due to climate change. Standard sequencing methods to profile soil microbiomes cannot determine whether community shifts are driven by increases in select members, losses of others, or masked by large pools of relic DNA. Instead, researchers used quantitative stable isotope probing with 18O-water to estimate the in situ growth rates of individual bacterial taxa under long-term elevated CO2 and across a gradient of warming treatments in a northern Minnesota peat bog at the SPRUCE (Spruce and Peatland Responses Under Changing Environments) experiment, representing a particularly vulnerable terrestrial carbon reservoir.

The microbial communities at SPRUCE have been subjected to experimental conditions for more than four years, and therefore had ample time to acclimate to the treatments. Researchers found that a large proportion of bacterial taxa displayed little to no growth across temperatures under ambient CO2 concentrations, but faster growth under certain temperatures with elevated CO2, highlighting a strong interplay between warming and CO2 concentrations. Growth responses of multiple taxa could be clustered into three response patterns under ambient CO2, and just two response patterns under elevated CO2. Elevated CO2 shifted the temperature of maximum growth for the two dominant lineages of the peat microbiome. The temperature of maximum growth among Proteobacteria increased under elevated CO2, contrasting the Acidobacteria whose maximum growth temperature decreased. Researchers found support for phylogenetic conservation of growth patterns among Acidobacteria and Proteobacteria at approximately the genus-level under ambient, but not elevated CO2. Among Proteobacteria, groups with tight plant associations such as Rhizobiales (N-fixing symbionts) exhibited enhanced growth only at elevated temperature and CO2, suggesting these microorganisms may benefit from increases in rhizodeposition. These results suggest that certain taxa may be predisposed for growth under altered climate conditions, with a disproportionate influence on carbon cycling and peatland feedbacks to climate change.

Northern peatlands are also of interest due to their exceedingly low inorganic nitrogen (N) contents and reliance on organic N. As such researchers have additionally leveraged peat collected from SPRUCE to conduct a laboratory incubation to explore the interactive effects of N source and temperature on nutrient assimilation and growth. Researchers used multiple isotope tracers to characterize either microbial growth (18O-water) or N assimilation with three different substrates representing inorganic (15N-ammonium and 15N-nitrate) and organic (15N-glutamate) sources. Metabolomics profiles using FT-ICR indicate significant similarities among unique metabolites across the N treatments relative to controls. N-amendment increased the richness of molecules classed as condensed hydrocarbons (less bioavailable) at 25oC while decreasing richness of protein-like (more bioavailable) molecules at 15oC relative to matched unamended controls. Further, the average metabolite pool contained less potential energy at 25oC, across all N amendments as well as control soils. Preliminary results reveal a significant impact of both temperature and substrate at the bulk level on respiration and N assimilation into microbial biomass, with respiration most strongly impacted by glutamate amendment but N-assimilation into microbial biomass highest under ammonium amendment. Ongoing work to generate taxon-specific growth rates and nutrient use efficiencies will be used to clarify whether differences at the bulk level are driven by the differential responses of individual taxa, and SIP-metagenomes and SIP-proteomes will be leveraged to explore altered metabolism and nutrient allocation under the treatments.

Together these experiments reveal how individual microorganisms vary in their acquisition, use, and release of nutrients—attributes that directly impact the rate and fate of environmental nutrient transformations in a globally important ecosystem.

Funding Information

This research was supported by a grant from the Department of Energy’s Biological Systems Science Division Program in Genomic Science (No. DE-SC0020172, FWP 77475). Research conducted at the Pacific Northwest National Laboratory was conducted under the auspices of U.S. Department of Energy Contract DE-AC05-76RL01830. Work at Lawrence Livermore National Laboratory was performed under U.S. Department of Energy Contract DE-AC52-07NA27344.