Excessive use of chemical fertilizers in agricultural practices have demonstrated a significant impact on microbial diversity and community in soil by altering soil physical and chemical properties, thereby leading to a certain degree of soil salinization and nutritional imbalances. As an organic amendment, maize straw has been widely used to improve soil quality; however, its effect on the soil bacterial community remains limited in Calcarie-Fluvie Cambisols soil in semi-humid arid plateau of North China. In the present experiment, we investigated the effects of continuous straw utilization and fertilization on bacterial communities in Shouyang, Shanxi province, China. Soil samples were collected from 5 different straw utilization and fertilization modes in the following ways: straw mulching (SM), straw crushing (SC), cattle manure (CM), in which way straw is firstly used as silage and then organic fertilizer, control with no straw return (NSR), and control without fertilizers (CK), same amount of N+P fertilizer was applied to the regimes except CK. High-throughput sequencing approaches were applied to the V3-V4 regions of the 16S ribosomal RNA for analysis of the bacterial abundance and community structures. Different long-term straw returning regimes significantly altered the physicochemical properties and bacterial communities of soil, among which CM had the most significant effects on soil fertility and bacterial diversity. Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes were consistently dominant in all soil samples, and Redundancy analysis (RDA) showed significant association of total nitrogen (TN), total phosphorus (TP) and available potassium (AK) with alternation of the bacterial community. Cattle manure had the most beneficial effects on soil fertility and bacterial diversity among different straw utilization and fertilization modes.

Soil eukaryotic microorganisms are important to biodiversity, and returning different kinds of organic materials to the field could improve the biodiversity of soil eukaryotic microorganisms. However, no detailed research has been conducted in the northern China semi-arid area in returning the different organic materials to the field and determining the status of eukaryotic microorganisms. Therefore, we explored the effects of various organic materials returning to the soil in combination with inorganic fertilizer on the diversity and community structure of eukaryotic microorganisms in Shanxi province, China. Soil samples were collected from five different fertilization treatments: chemical fertilizer (F), chemical fertilizer + cattle manure (FM), chemical fertilizer + straw (FS), chemical fertilizer + pig manure (FC) and control without fertilizers (CK). High-throughput sequencing was applied to analyze the eukaryotic diversity and community structure. Results showed that the dominant eukaryotic microorganisms among soil samples were Fungi, Viridiplantae, Metazoa and Protist. Although α-diversity was not significantly different among the five treatments, principal coordinate analysis and permutational multivariate analysis of variance illustrated significant differences (p < 0.001) in β-diversity of eukaryotic microorganism under treatments with different organic materials. Redundancy analysis showed that the soil properties, including total potassium, available nitrogen, available potassium and organic matter were the main factors attributed to eukaryotic microorganisms’ community structure in this region.

The scarcity and uneven distribution of precipitation present significant challenges for agriculture in arid regions. Fertilization can improve crop yields and water productivity (WP) under these conditions. However, the effects of different long-term fertilization practices on maize yield and WP under varying precipitation patterns require further research. A 30-year fertilization experiment was conducted to investigate the effects of different fertilization treatments on maize yield, WP, soil organic carbon (SOC), and the correlations among these factors. The treatments included no fertilization, application of chemical fertilizers alone, combined application of chemical fertilizers and cattle manure, and application of a high amount of cattle manure alone. Chemical fertilizers, cattle manure, and the combined application of chemical fertilizers and cattle manure significantly increased maize yield by 61.81–86.14%, 121.0%, and 114.5–125.5%, and increased WP by 59.4–84.9%, 119.4%, and 111.9–126.5%, respectively, compared to the unfertilized control. The combined application of chemical fertilizers and cattle manure resulted in optimal maize yield and WP, while also substantially reducing the coefficient of variation in maize yield (by 19.9–25.9% compared to the control) under interannual precipitation fluctuations. Compared with the no fertilization treatment, the average increase in maize yield peaks in very wet years, while WP reaches its highest level in relatively dry years. Maize yield was significantly positively related to SOC, WP, and water consumption during growth (p < 0.01). SOC was also significantly positively correlated with WP (p < 0.01). For every unit increase in SOC, the WP increased by 0.3955 kg ha⁻¹ mm⁻¹. In summary, the integrated application of organic and inorganic fertilizers is a proven strategy to enhance crop productivity and resilience, while concurrently improving WP and SOC. This synergistic approach represents a cornerstone for climate-resilient and sustainable dryland agriculture.

The overuse of antibiotics has led to the dissemination of antibiotic resistance genes (ARGs) in agricultural ecosystems, posing a threat to food safety. While current research on ARG transfer in soil–crop systems mainly concerns raw-consumed vegetables like lettuce, its impact on staple crops remains insufficiently studied. This study investigates how organic fertilizer affects ARG dissemination in the soil–millet system. Four fertilization treatments were established: no fertilization (CK), chemical fertilizer only (F), chemical fertilizer combined with manure (FM1), and chemical fertilizer combined with double amount of manure (FM2). Samples were collected from millet rhizosphere soil, roots, stems, leaves, and grains. High-throughput quantitative PCR was employed to investigate the transfer and dissemination of ARGs across the soil–millet system. Results showed that a total of 130 ARGs and 13 mobile genetic elements (MGEs), belonging to 17 gene families, were detected across all samples. The number of unique ARGs was higher in treatments FM1 and FM2 with manure. The accumulated absolute abundances of ARGs, MGEs and gene families all showed an order of FM1 > CK > FM2 > F. Pearson correlation analysis showed a close correlation among ARGs and MGEs. Although organic fertilizer application increased the absolute abundance of ARG-related genes in the rhizosphere soil and millet tissues, posing a potential threat to food safety, the rational strategy employed in the FM1 treatment effectively reduced ARG accumulation in millet leaves and grains. Therefore, this optimized application rate is recommended for millet production.