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.

Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C4 grassland soils

“…AOB population dynamics were related to soil moisture in our study. The significant negative correlation of amoA gene abundance but positive correlation of amoA transcript abundance with SWC found in this study was also observed in a cotton field in the similar climatic zone ( Hu et al, 2021a ). One possible explanation was that increasing SWC decreases soil oxygen, resulting in decreased abundances of aerobic AOB.…”

“…Quantitative PCR (qPCR) of AOB amoA genes and transcripts were performed on a CFX96 Optical Real-Time Detection System (Bio-Rad, Laboratories Inc., Hercules, CA, USA) using the primer pair amoA -1F (5′- GGGGTTTCTACTGGTGGT -3′) and amoA -2R (5′- CCCCTCKGSAAAGCCTTCTTC -3′) ( Rotthauwe, Witzel & Liesack, 1997 ) as we have previously described ( Hu et al, 2021a ).…”

Nitrogen Fertilization and Native C4 Grass Species Alter Abundance, Activity, and Diversity of Soil Diazotrophic Communities

“…Ten-fold serial dilutions (10 2 to 10 8 copies μl –1 ) of the plasmids containing nifH genes made through molecular cloning by the TOPO TA Cloning kit (Thermo Scientific, CA, United States) were used during qPCR assays to generate standard curves for quantifying nifH genes and transcripts in soil samples. Plasmids containing nifH genes amplified from environmental samples, described in our previous study ( Hu et al, 2021 ), were used as standards. Following the reactions, a melt curve analysis was performed to confirm the specificity of the PCR product.…”

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories

“…Moreover, land tilling also affects the abundance of genes involved in several stages of nitrogen fixation [ 52 ]. Under low N fertilization (67 kg ha −1 ), Hu et al [ 53 ] reported that the relative abundance of the nif H transcript was higher in no-till soils than in conventionally tilled soils. Furthermore, the influence of soil management was also observed in the abundance of genes involved in nitrification ( amo A) and denitrification ( nor B, nir K, and nir S) in the soils.…”

“…Furthermore, the influence of soil management was also observed in the abundance of genes involved in nitrification ( amo A) and denitrification ( nor B, nir K, and nir S) in the soils. Hu, Jin, Konkel, Schaeffer, Schneider and DeBruyn [ 53 ] studied the effects of agricultural management on the abundance of genes involved in nitrogen cycling. They observed that under N fertilizer treatment (67 kg ha −1 ), both the relative abundance and transcript of the amo A gene was increased in no-till soils.…”