Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO2

David Rosado-Porto; Stefan Ratering; Gerald Moser; Marianna Deppe; Christoph Müller; Sylvia Schnell

doi:10.3389/fmicb.2022.937021

Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO₂

Front Microbiol. 2022 Aug 23:13:937021. doi: 10.3389/fmicb.2022.937021. eCollection 2022.

Authors

David Rosado-Porto^{1

2}, Stefan Ratering¹, Gerald Moser³, Marianna Deppe³, Christoph Müller^{3

4}, Sylvia Schnell¹

Affiliations

¹ Institute of Applied Microbiology, Justus Liebig University, Giessen, Germany.
² Faculty of Basic and Biomedical Sciences, Simón Bolívar University, Barranquilla, Colombia.
³ Institute of Plant Ecology, Justus Liebig University, Giessen, Germany.
⁴ School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland.

Abstract

Soil organisms play an important role in the equilibrium and cycling of nutrients. Because elevated CO₂ (eCO₂) affects plant metabolism, including rhizodeposition, it directly impacts the soil microbiome and microbial processes. Therefore, eCO₂ directly influences the cycling of different elements in terrestrial ecosystems. Hence, possible changes in the cycles of carbon (C), nitrogen (N), and sulfur (S) were analyzed, alongside the assessment of changes in the composition and structure of the soil microbiome through a functional metatranscriptomics approach (cDNA from mRNA) from soil samples taken at the Giessen free-air CO₂ enrichment (Gi-FACE) experiment. Results showed changes in the expression of C cycle genes under eCO₂ with an increase in the transcript abundance for carbohydrate and amino acid uptake, and degradation, alongside an increase in the transcript abundance for cellulose, chitin, and lignin degradation and prokaryotic carbon fixation. In addition, N cycle changes included a decrease in the transcript abundance of N₂O reductase, involved in the last step of the denitrification process, which explains the increase of N₂O emissions in the Gi-FACE. Also, a shift in nitrate ( ${NO}_{3}^{-}$ ) metabolism occurred, with an increase in transcript abundance for the dissimilatory ${NO}_{3}^{-}$ reduction to ammonium ( ${NH}_{4}^{+}$ ) (DNRA) pathway. S metabolism showed increased transcripts for sulfate ( ${SO}_{4}^{2 -}$ ) assimilation under eCO₂ conditions. Furthermore, soil bacteriome, mycobiome, and virome significantly differed between ambient and elevated CO₂ conditions. The results exhibited the effects of eCO₂ on the transcript abundance of C, N, and S cycles, and the soil microbiome. This finding showed a direct connection between eCO₂ and the increased greenhouse gas emission, as well as the importance of soil nutrient availability to maintain the balance of soil ecosystems.

Keywords: FACE; carbon cycle; elevated CO2; functional metatranscriptomics; nitrogen cycle; soil microbiome; sulfur cycle.