Changes in Foxtail Millet (Setaria italica L.) Yield, Quality, and Soil Microbiome after Replacing Chemical Nitrogen Fertilizers with Organic Fertilizers

Foxtail millet (Setaria italica L.) is one of the most economically valuable drought-resistant crops in arid and semi-arid regions as a nutrition health crop, which has garnered considerable research attention. We evaluated the effects of replacing chemical nitrogen fertilizers with organic fertilizers on two primary plant accessions of foxtail millet (Dungu and Jinfen no. 2). Nitrogen in a standard fertilizer was replaced with organic fertilizer at application levels of 0, 25, 50, 75, and 100%, with effects on crop yield, quality (appearance, taste, and nutritional value), and soil microbiome, assessed using field cultivation experiments. Our results indicate that partial replacement of conventional fertilizers with organic fertilizers improved both yield and quality. Specifically, the 75% replacement significantly improved the appearance (yellow pigment content and grain diameter) and taste (amylose content and soluble sugar content) of foxtail millet, while the 50% replacement significantly improved the taste (gel consistency) and nutritional qualities (crude protein content and seven amino acids’ content). The 50% replacement of organic fertilizer regulated amino acid content more significantly than starch content. Increased ratios of organic fertilizer significantly reduced the soil pH by 0.03–0.36 and increased the relative abundance of Chloroflexi as well as that of Basidiomycota and Cercozoa in the soil microbiome. Our findings provide a solid theoretical foundation for subsequent studies on fertilizer use for foxtail millet and contribute to developing functional nutritional foods in the foxtail millet industry.