Diversity of nitrogen cycling genes at a Midwest long-term ecological research site with different management practices

Abstract

Nitrogen fertilizer results in the release of nitrous oxide (N 2 O), a concern because N 2 O is an ozone-depleting substance and a greenhouse gas. Although the reduction of N 2 O to nitrogen gas can control emissions, the factors impacting the enzymes involved have not been fully explored. The current study investigated the abundance and diversity of genes involved in nitrogen cycling (primarily denitrification) under four agricultural management practices (no tillage [NT], conventional tillage [CT], reduced input, biologically-based). The work involved examining soil shotgun sequencing data for nine genes (napA, narG, nirK, nirS, norB, nosZ, nirA, nirB, nifH). For each gene, relative abundance values, diversity and richness indices, and taxonomic classification were determined. Additionally, the genes associated with nitrogen metabolism (defined by the KEGG hierarchy) were examined. The data generated were statistically compared between the four management practices. The relative abundance of four genes (nifH, nirK, nirS, and norB) were significantly lower in the NT treatment compared to one or more of the other soils. The abundance values of napA, narG, nifH, nirA, and nirB were not significantly different between NT and CT. The relative abundance of nirS was significantly higher in the CT treatment compared to the others. Diversity and richness values were higher for four of the nine genes (napA, narG, nirA, nirB). Based on nirS/nirK ratios, CT represents the highest N 2 O consumption potential in four soils. In conclusion, the microbial communities involved in nitrogen metabolism were sensitive to different agricultural practices, which in turn, likely has implications for N 2 O emissions. Key points• Four genes were less abundant in NT compared to one or more of the others soils (nifH, nirK, nirS, norB).• The most abundant sequences for many of the genes classified within the Proteobacteria.• Higher diversity and richness indices were observed for four genes (napA, narG, nirA, nirB).• Based on nirS/nirK ratios, CT represents the highest N 2 O consumption potential.

Bridging the gap between agriculture and climate: Mitigation of nitrous oxide emissions from fertilizers

“…16 Similarly, Zheng and Cupples concluded that the relative abundance of certain nitrogen-cycle genes were affected by agricultural practices. 17 Therefore, there must be a careful balance between agricultural practices, soil nitrogen content, and the microbial community, and further studies regarding these interactions could uncover the variables and mechanisms.…”

“…Behnke et al showed that crop rotation and cover crop use, which are common conservation practices that introduce nitrogen to the soil, alter the nitrogen cycle directly or indirectly thus impacting nitrous oxide generation 16 . Similarly, Zheng and Cupples concluded that the relative abundance of certain nitrogen‐cycle genes were affected by agricultural practices 17 . Therefore, there must be a careful balance between agricultural practices, soil nitrogen content, and the microbial community, and further studies regarding these interactions could uncover the variables and mechanisms.…”

A Longitudinal Study of the Microbial Basis of Nitrous Oxide Emissions Within a Long-Term Agricultural Experiment

“…Chisel tillage increased all microbial N cycle genes (nifH, nirK, nirS, and nosZ) compared to no-till (Table 2). In a study from the Kellogg Biological Station in Michigan, each denitrification gene was also reduced in the no-till treatment compared to conventional tillage (Li and Cupples, 2021). Chisel tillage is used to help break down residues, which stimulates microbial activity through aeration and warmer soil conditions (Balesdent et al, 2000;Martens, 2000;Hu et al, 2021).…”

“…Without fertilization, the leguminous cover crop, hairy vetch, contained similar N cycle gene expression as the fertilized no cover treatment (Hu et al, 2021). In a Michigan, USA study, Li and Cupples (2021) observed different tillage treatments within a corn-soybean-wheat rotation and found that no-till decreased copy numbers for each denitrification gene (nirK, nirS, and nosZ) compared to conventional tillage.…”