Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community

Abstract

Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four time points that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased the transcription of genes encoding ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen-fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.IMPORTANCE A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for an improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.

Keywords: carbon metabolism; metagenomics; metatranscriptomics; microbial ecology; nitrogen fixation; nitrogen metabolism; nitrogen regulation; nutrient transport; soil microbiology.

FIG 1

Mean concentrations (± standard errors [SE]) of nitrate (A) and ammonium (B) and rates of carbon dioxide production (C) and K₂SO₄-extractable C (D) as a function of time after glucose amendments.

FIG 2

Nonmetric multidimensional scaling (NMDS) using Bray-Curtis distance of normalized KEGG annotation abundances for metagenomes (top) and metatranscriptomes (bottom) 0, 8, 24, and 48 h after the addition of glucose.

FIG 3

(A) Log₂ fold changes (mean LFCs ± SE) relative to t₀ of normalized gene (left) and transcript (right) abundances versus normalized counts for N cycling genes from glucose-amended soils. LFCs and normalized counts represent the averages between t₈, t₂₄, and t₄₈ for each gene. (B) Log₂ fold changes in transcript abundances for genes grouped by biologically relevant reactions and pathways. A black asterisk indicates a significant change relative to t₀. MFS, major facilitator superfamily.

FIG 4

Relative transcript abundances of major taxa for reactions and pathways of N cycling 0, 8, 24, and 48 h after glucose amendments.

FIG 5

Abundances and log₂ fold changes of transcripts 8 h after glucose addition for C and N metabolism, including glycolysis, the TCA cycle, the N regulatory network, and GS-GOGAT. Color represents log₂ fold changes of transcript abundances relative to t₀, and size indicates the number of transcripts. Thin black arrows indicate reactants or products of pathways, and gray arrows represent regulatory controls. Gene names are presented in white boxes (for example, glnA), whereas pathway or enzyme names are presented in boldface type (for example, GS or glycolysis).