Limited Impacts of Cover Cropping on Soil N-Cycling Microbial Communities of Long-Term Corn Monocultures

Abstract

Cover cropping (CC) is a promising in-field practice to mitigate soil health degradation and nitrogen (N) losses from excessive N fertilization. Soil N-cycling microbial communities are the fundamental drivers of these processes, but how they respond to CC under field conditions is poorly documented for typical agricultural systems. Our objective was to investigate this relationship for a long-term (36 years) corn [Zea mays L.] monocultures under three N fertilizer rates (N0, N202, and N269; kg N/ha), where a mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth.] was introduced for two consecutive years, using winter fallows as controls (BF). A 3 × 2 split-plot arrangement of N rates and CC treatments in a randomized complete block design with three replications was deployed. Soil chemical and physical properties and potential nitrification (PNR) and denitrification (PDR) rates were measured along with functional genes, including nifH, archaeal and bacterial amoA, nirK, nirS, and nosZ-I, sequenced in Illumina MiSeq system and quantified in high-throughput quantitative polymerase chain reaction (qPCR). The abundances of nifH, archaeal amoA, and nirS decreased with N fertilization (by 7.9, 4.8, and 38.9 times, respectively), and correlated positively with soil pH. Bacterial amoA increased by 2.4 times with CC within N269 and correlated positively with soil nitrate. CC increased the abundance of nirK by 1.5 times when fertilized. For both bacterial amoA and nirK, N202 and N269 did not differ from N0 within BF. Treatments had no significant effects on nosZ-I. The reported changes did not translate into differences in functionality as PNR and PDR did not respond to treatments. These results suggested that N fertilization disrupts the soil N-cycling communities of this system primarily through soil acidification and high nutrient availability. Two years of CC may not be enough to change the N-cycling communities that adapted to decades of disruption from N fertilization in corn monoculture. This is valuable primary information to understand the potentials and limitations of CC when introduced into long-term agricultural systems.

Keywords: N cycle genes; N fertilization; amoA; maize (Zea mays L.); nifH; nirK; nirS; nosZ.

FIGURE 1

Location and coordinates of the experimental site within the United States and the state of Illinois.

FIGURE 2

Treatment means of soil microbial marker genes (log₁₀ copies/μg DNA), including bacterial (Bacteria) and archaeal (Archaea) 16S rRNA, fungal ITS region (Fungi), nifH, archaeal (AOA) and bacterial (AOB) amoA, nirK, nirS, and nosZ-I separated by N fertilization rate (Nrate), with their standard errors of the mean as whiskers. Asterisks indicate the level of significance associated with the probability value from analysis of variance of the factors (*p < 0.1, **p < 0.05). Nrate treatment levels were: 0, 202, and 269 kg N/ha.

FIGURE 3

The treatment means of soil microbial marker genes in log₁₀ (copies/μg DNA), including bacterial (Bacteria) and archaeal (Archaea) 16S rRNA, fungal ITS region (Fungi), nifH, archaeal (AOA) and bacterial (AOB) amoA, nirK, nirS, and nosZ-I separated by cover cropping (CC), with their standard errors of the mean as whiskers. The CC treatment levels were bare fallow control (BF) and hairy vetch and cereal rye cover crop mixture (CC).

FIGURE 4

The treatment means of soil microbial marker genes in (log₁₀ copies/μg DNA), including bacterial (Bacteria) and archaeal (Archaea) 16S rRNA, fungal ITS region (Fungi), nifH, archaeal (AOA) and bacterial (AOB) amoA, nirK, nirS, and nosZ-I separated by the interactions between N fertilization rate (Nrate) and cover cropping (CC), with their standard errors of the mean as whiskers. The asterisks indicate the probability value of the treatment effect from analysis of variance (**p < 0.05). Nrate treatment levels were: 0, 202, and 269 kg N/ha. CC treatment levels were bare fallow control (BF) and hairy vetch and cereal rye cover crop mixture (CC).

FIGURE 5

Heatmap depicting the matrix of Spearman’s rank correlation coefficients among the soil microbial marker genes, soil properties, and potential nitrification (PNR) and denitrification (PDR) rates. Marker genes included bacterial (Bacteria) and archaeal (Archaea) 16S rRNA, fungal ITS region (Fungi), nifH, archaeal (AOA) and bacterial (AOB) amoA, nirK, nirS, and nosZ-I. Soil properties included cation exchange capacity (CEC, cmol_c/kg), pH, soil organic matter (SOM,%), bulk density (Bd, Mg/m³), water aggregate stability (WAS,%), ammonium (NH₄, mg/kg), nitrate (NO₃, mg/kg), available phosphorus (Pbray, mg/kg), and extractable potassium (K, mg/kg). The red and blue hues each indicate positive and negative associations, respectively. Higher color saturation indicates greater absolute values of Spearman’s rank correlation coefficients.