Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity

Abstract

Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the population size (gene copy abundances) and functional activity (transcript copy abundances) of five bacterial genes involved in soil N cycling (ammonia-oxidizing bacteria [AOB] amoA, nifH, nirK, nirS, and nosZ) in a long-term continuous cotton production system under different management practices (cover crops, tillage, and inorganic N fertilization). Hairy vetch (Vicia villosa Roth), a leguminous cover crop, most effectively promoted the expression of N cycle genes, which persisted after cover crop termination throughout the growing season. Moreover, we observed similarly high or even higher N cycle gene transcript abundances under vetch with no fertilizer as no cover crop with N fertilization throughout the cover crop peak and cotton growing seasons (April, May, and October). Further, both the gene and transcript abundances of amoA and nosZ were positively correlated to soil nitrous oxide (N₂O) emissions. We also found that the abundances of amoA genes and transcripts both positively correlated to field and incubated net nitrification rates. Together, our results revealed relationships between microbial functional capacity and activity and in situ soil N transformations under different agricultural seasons and soil management practices.IMPORTANCE Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer. Hairy vetch also left a legacy on soil nutrient capacity by promoting the continued activity of N cycling microbes after cover crop termination and into the main growing season. By examining both genes and transcripts involved in soil N cycling, we showed different responses of functional capacity (i.e., gene abundances) and functional activity (i.e., transcript abundances) to agricultural seasons and management practices, adding to our understanding of the effects of soil health management practices on microbial ecology.

Keywords: agroecosystems; conservation agriculture; denitrification; nitrification; nitrogen fixation; quantitative PCR (qPCR); quantitative reverse transcription PCR (qRT-PCR); soil health; soil microbes; soil microbiology; soil nitrogen cycle.

FIG 1

Seasonal dynamics of 16S rRNA gene normalized nifH, amoA, nirK, nirS, and nosZ gene abundances (A) and absolute abundances of nifH, amoA, nirK, nirS, nosZ, and 16S rRNA genes (B) in relation to tillage. Points represent the mean ± standard error (n = 24). NT, no tillage; CT, conventional tillage.

FIG 2

Variation of 16S rRNA gene normalized nifH, amoA, nirK, nirS, and nosZ gene abundances (A) and absolute abundances of nifH, amoA, nirK, nirS, nosZ, and 16S rRNA genes (B) in relation to N fertilization rate (0N, no N fertilization; 67N, 67 kg N ha⁻¹ fertilization) under different cover crop treatments (NC, no cover; V, vetch; W, wheat). Points represent the mean ± standard error (n = 32).

FIG 3

Seasonal dynamics of 16S rRNA normalized transcript abundances of nifH, amoA, nirK, nirS, and nosZ (A) and absolute transcript abundances of nifH, amoA, nirK, nirS, nosZ, and 16S rRNA gene (B) in relation to cover crops and tillage. Points represent the mean ± standard error (n = 8). NC, no cover; V, vetch; W, wheat; NT, no tillage; CT, conventional tillage.

FIG 4

Seasonal dynamics of 16S rRNA normalized transcript abundances of nifH, amoA, nirK, nirS, and nosZ (A) and absolute transcript abundances of nifH, amoA, nirK, nirS, nosZ, and 16S rRNA gene (B) in relation to cover crop treatments and N fertilization rate. Points represent the mean ± standard error (n = 8). NC, no cover; V, vetch; W, wheat; 0N, no N fertilization; 67N, 67 kg N ha⁻¹ fertilization.

FIG 5

Seasonal dynamics of transcript/gene ratio of nifH, amoA, nirK, nirS, and nosZ (B) in relation to cover crops and tillage (A) and in relation to cover crops and N fertilization (B). Points represent the mean ± standard error (n = 8). NC, no cover; V, vetch; W, wheat; NT, no tillage; CT, conventional tillage.

FIG 6

NMDS of Bray-Curtis distances between N cycling communities based on abundances of five N cycling genes (G) and transcripts (T) (stress = 0.015). Points on the ordination plots are colored by season (A), cover crop treatment (B), tillage (C), and fertilization rate (D). NC, no cover; V, vetch; W, wheat; NT, no tillage; CT, conventional tillage; 0N, no N fertilization; 67N, 67 kg N ha⁻¹ fertilization. Ellipses represent 95% confidence interval of each group.

FIG 7

Heatmap showing correlation among genes, gene transcripts, transcript/gene ratios, and soil properties. SWC, soil water content; TC, total carbon; TN, total nitrogen; TEC, total extractable carbon; TEN, total extractable nitrogen; MBC, microbial biomass carbon; MBN, microbial biomass nitrogen.