Uncovering the Microbial Food Web in Thawing Permafrost

The Science

Near-surface permafrost may be nearly lost by the end of the century. Thawing releases carbon that’s consumed by microbes in the soil. The activity of these microbes, in turn, gives off carbon dioxide and methane. How can we predict how much is released without understanding more about the microbes involved? An international team of scientists identified the genomes of more than 1,500 of these microbes and discovered their potential for eating soil carbon.

The Impact

This study offers insights into the fate of soil carbon as permafrost peatlands thaw. It also shows that even complex microbial communities can now be examined via a genome-centric approach. The approach provides a new analytic framework to understand microbes’ ecology and function.

Summary

Large amounts of soil carbon sequestered in permafrost are becoming available for microbial degradation as permafrost thaws. Its fate is unclear; will it remain stably stored in the soil, or will it be metabolized into the greenhouse gases carbon dioxide or methane? Understanding the carbon processing of microbial communities in thawing permafrost is thus of considerable importance to accurately predicting the magnitude of climate feedback from these systems. However, little is known about these microorganisms because very few can be grown in the laboratory. In this study, a multinational group of researchers applied new sequencing and computational techniques to recover near-complete genomes of microorganisms directly from a permafrost thaw gradient in Stordalen Mire, northern Sweden. Genes encoded on the recovered genomes showed which microorganisms were capable of performing each step of the degradation of soil organic matter, from complex polysaccharides through to carbon dioxide and methane. The correlation of specific lineages indicated potential metabolic cooperation, while other lineages co-varied with the dissolved methane-to-carbon-dioxide ratio, an important parameter in global climate models, and with methane isotopic signatures, a parameter used to partition methane production sources in atmospheric inversion models. Further study is required to elucidate more fully the functions and changes of the microbes, and to distill the insights for use in climate models.

Funding

The study was funded by the Genomic Science Program in the Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research (BER); Australian Research Council Discovery Early Career Research Awards; Australian Government Research Training Program Scholarships; and Australian Research Council Future Fellowship. A portion of the research was performed using Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility, and a portion was performed under the Facilities Integrating Collaborations for User Science initiative with resources at both the DOE Joint Genome Institute and EMSL. Both facilities are sponsored by BER.

Publications

B.J. Woodcroft, C.M. Singleton, J.A. Boyd, et al., “Genome-centric view of carbon processing in thawing permafrost.” Nature 560, 49 (2018). [DOI: 10.1038/s41586-018-0338-1]