PRJNA669067
Prosser soil metagenome raw sequence reads
The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching, and emissions of N2O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analyzed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons, and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass, and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared to the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, AOA, and AOB increased in abundance with intercropping and (for AOA/AOB) fertilization. However, only AOB abundance in fertilized plots significantly correlated to N2O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization. Gene sequences representing novel taxa related to the Nitrosovibrio tenuis and Nitrosospira were also recovered.