Using Metatranscriptomics to Understand Carbon Decomposition in Forest Soils

Forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi.

The Science

Decomposition of plant materials in soils is accomplished by a complex and highly diverse community of microorganisms. The vast majority of these microbes cannot be grown in laboratories, and the roles of different species in decomposition and responses to changing environmental conditions are not well understood. Ecologists have demonstrated that the addition of nitrogen to forest soils significantly slows the rate of carbon decomposition, but it is not well understood why this change occurs. Recent advances in soil metatranscriptomics, the direct analysis of microbial community gene expression in environmental samples, have provided researchers with a more sophisticated set of tools to track changes in microbial community structure and function. In a new study, a collaborative team of scientists at Los Alamos National Laboratory and the University of Michigan have completed a metatranscriptomic analysis of forest soils at a long-term ecological experiment examining impacts of nitrogen addition. By developing a new technique for metatranscriptomic sampling, the team was able to complete a much deeper analysis of community metabolic potential than has been previously attempted. Researchers generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Using this approach, fungal and bacterial genes involved in degradation of plant lignocellulose were determined to undergo large changes in expression at two separated sites with elevated nitrogen.

The Impact

Overall pattern shifts were consistent with decreased carbon decomposition rates, but specific mechanisms appeared to vary between the different forest sites. As climate change processes shift environmental variables and agricultural practices continue to alter nitrogen inputs in terrestrial soils, understanding their coupled impacts on microbial community activities will be crucial to more confidently modeling and predicting impacts on different ecosystems.

BER Program Manager

Dawn Adin

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Hesse, C. N., R. C. Mueller, M. Vuyisich, L. Gallegos-Graves, C. D. Gleasner, D. R. Zak, and C. R. Kuske. 2015. “Forest Floor Community Metatranscriptomics Identify Fungal and Bacterial Response to N Deposition in Two Maple Forests,” Frontiers in Microbiology. DOI: 10.3389/fmicb.2015.00337.