Abstract
Cover crops (CC) have demonstrated beneficial effects on several soil properties yet questions remain regarding their effects on soil microbial communities. Among them, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) have a key role for N cycling in soil and their responses in the rhizosphere of terminated CC deserve further investigation. A greenhouse experiment was established to assess N fertilization (with or without N) and termination methods (glyphosate, mowing, and untreated control) of common oat (Avena sativa L.) as potential drivers of AOA and AOB responses in the rhizosphere. The abundance of amoA genes was determined by quantitative real-time PCR (qPCR), the community structure was assessed with Illumina amplicon sequencing of these genes, while the function was assessed from potential nitrification activity (PNA). While N fertilization had no influence on AOA, the termination method significantly increased amoA gene copies of AOA in mowed plants relative to glyphosate termination or the untreated control (1.76 and 1.49-fold change, respectively), and shifted AOA community structure (PERMANOVA, p<0.05). Ordination methods indicated a separation between AOA communities from control and glyphosate-terminated plants relative to mowed plants for both UniFrac and Aitchison distance. Converserly, N fertilization significantly increased AOB abundance in the rhizosphere of mowed and control plants, yet not in glyphosate-treated plants. Analyses of community structure showed that AOB changed only in response to N fertilization and not to the termination method. In line with these results, significantly higher PNA values were measured in all fertilized samples, regardless of the termination methods. Overall, the results of this study indicated that bacterial and archaeal nitrifiers have contrasting responses to fertlization and plant termination methods. While AOA were responsive to the termination method, AOB were more sensitive to N additions, although, the stimulative effect of N fertilization on amoAAOB abundance was dependent on the termination method.
Highlights
One of the biggest challenges of modern agriculture is the production of enough high-quality food, while reducing the environmental impact and the dependence on external inputs
Mowing resulted in a higher amoAAOA abundance in the rhizosphere compared to control plants (1.49-fold change, p < 0.01), and to those terminated with glyphosate (1.76-fold change, p < 0.001)
While no N-induced stimulation of ammonia-oxidizing bacteria (AOB) was observed in glyphosate-treated plants, a significantly greater amoA copy number was observed after N fertilization in the rhizosphere of mowed and control plants relative to the unfertilized plants (p < 0.05; lower case letters, Table 1; Supplementary Figure S1)
Summary
One of the biggest challenges of modern agriculture is the production of enough high-quality food, while reducing the environmental impact and the dependence on external inputs. In this context, cover crops (CCs) have gained popularity as a sustainable alternative with demonstrated beneficial effects on several soil properties (Lu et al, 2000; Chavarría et al, 2016). The termination of the CC growth is required to allow planting of the cash crop and includes both mechanical (e.g., rolling or mowing) and chemical methods (Lu et al, 2000). How CC management practices affect soil microbial communities and their functions has been comparatively less studied than the influence of more traditional agricultural practices on soil microorganisms
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