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A high-resolution view of the plant–microbe–mineral interactions affecting C-cycling in thawed permafrost soils

EMSL Project ID


Arctic permafrost soils store approximately one third of the world’s soil carbon, a stock equal to the Earth’s atmosphere. Warming and drying projected over this century will make this vast soil carbon pool vulnerable to decomposition. Despite observations that plant roots easily invade thawed permafrost and an understanding that roots and root exudates can stimulate soil organic matter (SOM) decomposition, there has been very little research exploring the aboveground–belowground interactions among plant productivity, microbial communities, and soil minerals that will drive arctic soil carbon dynamics. This unresolved permafrost–climate feedback has major implications for climate security. This project examines how plant–microbe–mineral interactions regulate the permafrost–climate feedback, and incorporates these new discoveries into model development, evaluation, and application.

We aim to determine how plants, microbial activity, and organo-mineral associations influence permafrost soil C balance. To address our hypothesis, we are performing a series of SIP-incubations and a plant–permafrost mesocosm experiment, all of which employ stable isotopes to trace the fate of carbon and to understand how microbes and minerals interact to affect the cycling of new plant inputs and old, permafrost carbon. With our existing design, we can assess the impact of plant root exudates on permafrost C-cycling, but we require the high-resolution chemistry and molecular tools available through EMSL and JGI to probe the chemical and molecular underpinnings of the trends. With these tools, we aim to better understand (1) the stability and chemistry of organic matter on mineral surfaces in permafrost, and whether stability and chemistry are affected by new plant inputs, (2) whether changes in organic matter–mineral associations are a result of transformations of minerals induced by the exudates, and (3) whether new plant inputs “prime” the metabolism of microorganisms to access mineral-associated organic matter, and what genetic mechanisms underpin this pattern.

The tools provided by the FICUS award allow us to understand the processes from the molecular and genomic scale, which we will integrate into our modeling approach at regional and global scales. We will access this understanding via analysis of our incubation and plant–permafrost mesocosm samples with Mössbauer Spectroscopy to study the effect of soil type and exudates on mineralogy; X-ray photon spectroscopy (XPS) to understand the chemical composition of organic matter associated with permafrost mineral surfaces; 1H-NMR, 13C-NMR, and Fourier-transform ion cyclotron resonance (FTICR MS) to investigate the chemistry of dissolved organic matter (DOM) and mineral-associated OM; IRMS to quantify the amount of root exudate carbon in DOM and mineral-associated OM; qSIP-metagenomics to understand how plant root intrusion alters the physiology and function of permafrost microbial communities; and metatranscriptomics to explore the genes responsible for the breakdown of exudates and SOM. We will integrate these findings into our modeling framework to resolve the interactions among plants, microbes, and minerals, which are critical to advancing fundamental understanding of biogeochemical processes in a warming and thawing Arctic.

Project Details

Project type
FICUS Research
Start Date
End Date


Principal Investigator

Jessica Ernakovich
University of New Hampshire


Caitlin Pries
Dartmouth College

Team Members

Hannah Holland-Moritz
University of New Hampshire

Fernando Montaño López
Dartmouth College

William Wieder
National Center for Atmospheric Research

Stuart Grandy
University of New Hampshire