This study investigated the effects of bio-organic fertilizer (BF) containing plant growth-promoting bacterium Bacillus velezensis SS-20 on soil properties, microbial community structure, and C/N cycle functional genes. The results showed that compared with chemical fertilizer (CF) and deactivated bio-organic fertilizer (BFD) treatments, BF significantly improved soil physicochemical properties. Soil pH, organic matter, total nitrogen, total potassium, and total phosphorus content under BF treatment were increased by 14.8%, 56.5%, 48.2%, 38.8%, and 58.4%, respectively, compared to the control; soil urease and sucrase activities increased by 3.5 and 2.4 times those of CF treatment, respectively. Meanwhile, BF increased pakchoi yield by 11.2% (vs. CF). BF treatment enhanced the relative abundance of beneficial bacteria Actinomycetota by 28.4% compared with the BFD treatment and raised that of fungi Ascomycota to 1.9 times that of the control. At the genus level, BF significantly enriched biocontrol-relevant genus Pseudogymnoascus, whose abundance reached three times that of CF treatment, while the abundance of potentially harmful genus Penicillium decreased by 82%. BF also led to a high degree of synergy in carbon and nitrogen cycles. Functional gene analysis indicated that BF down-regulated multiple carbon-degrading genes, increased organic nitrogen metabolism genes by 5.3%, and reduced denitrification genes by 13.3%. Overall, bio-organic fertilizer optimized the soil microenvironment, regulated the microbial community structure, and improved C/N use efficiency and plant growth by introducing functional microorganisms and organic matter.

The ecological rice–eel co-culture system is not only beneficial for enhancing productivity and sustainability in agriculture but also plays a crucial role in promoting environmental health. In the present study, based on the long-term positioning trial of the rice–eel co-culture system that began in 2016 and was sampled in 2023, the effects of reduced nitrogen fertilizer application on soil physico-chemical properties and the bacterial community were investigated. Treatments included a conventional regular fertilization treatment (RT), rice–eel co-culture system regular fertilization (IT), and nitrogen-reduction 10%, 30%, and 50% fertilization treatments (IT90, IT70, and IT50). Our research demonstrated the following: (1) Compared to RT, IT significantly increased soil water-stable macroaggregates (R0.25), mean weight diameter (MWD), geometric mean diameter (GMD), and available phosphorus content, with the increases of 15.66%, 25.49%, 36.00%, and 18.42%, respectively. Among the nitrogen-reduction fertilization treatments, IT90 showed the most significant effect. Compared to IT, IT90 significantly increased R0.25, MWD, GMD, and available nitrogen content, with increases of 4.4%, 7.81%, 8.82%, and 28.89%, respectively. (2) Compared to RT, at the phylum level, the diversity of Chloroflexi was significantly increased under IT and IT50, and the diversity of Gemmatimonadota was significantly increased under IT90, IT70, and IT50. The diversity of Acidobacteriota was significantly higher in IT90 and IT70 compared to IT. It was shown that the rice–eel co-culture system and nitrogen fertilizer reduction could effectively improve the degradation capacity of organic matter and promote soil nitrogen cycling. In addition, redundancy analysis (RDA) identified total phosphorus, total nitrogen, and available nitrogen (p = 0.007) as the three most important environmental factors driving changes in the bacterial community. (3) The functional prediction analysis of soil microbiota showed that, compared to RT, the diversity of pathways related to biosynthesis (carbohydrate biosynthesis and cell structure biosynthesis) and metabolism (L-glutamate and L-glutamine biosynthesis) was significantly higher under IT70, IT90, IT, and IT50 (in descending order). However, the diversity of pathways associated with degradation/utilization/assimilation (secondary metabolite degradation and amine and polyamine degradation) was significantly lower under all the rice–eel co-culture treatments. In conclusion, the rice–eel co-culture system improved soil physicochemical properties and the soil microbial environment compared with conventional planting, and the best soil improvement was achieved with 10% less N fertilizer application.

To improve the degradation rate of sulfamethoxazole (SMX) under hypoxic conditions in paddy fields during the flooding period, a laboratory microcosm experiment was established in this study to investigate the regulatory effect of straw return on the hypoxic degradation of SMX and its underlying microbial mechanisms. The results demonstrated that straw addition significantly promoted the hypoxic degradation of SMX. By the 10th day of the experiment, the residual SMX content in the straw-amended group was only 11.3% of that in the non-straw control group, and the average degradation rate throughout the experimental period was increased by 85.7%. Straw provided complex carbon sources, including organic carbon (e.g., starch, sugars, and humus) and cellulose, which not only reshaped the microbial community structure and created new ecological niches but also increased the microbial network density under SMX stress from 0.010 to 0.024. Acinetobacter, Bacillus, and Pseudomonas, which possess both straw decomposition and SMX degradation capabilities, sequentially became the dominant bacterial taxa. These dominant taxa can adapt to hypoxic fermentation in the flooded environment and co-metabolize SMX by activating the metabolic pathways of aromatic compounds and sugars. This study is expected to open up a novel approach for the remediation of SMX-contaminated flooded paddy fields and provide valuable innovative insights for technological breakthroughs and practical applications in related fields.

Soil salinization limits sustainable agriculture. This study used a citric acid–FeSO₄ method to create modified chicken manure biochar (MCMB) as a carrier for the plant growth-promoting Bacillus velezensis SS-20, forming a biochar-based microbial agent (JS). A pot experiment included four treatments: CK (control), SS (SS-20 only), JF (MCMB only), and JS (biochar-based agent). The JS treatment significantly improved pakchoi plant height and aboveground fresh weight by 26.33% and 76.62%, respectively, compared to CK. It also lowered soil pH, electrical conductivity (EC), and salt content, while enhancing soil catalase activity by 8.83%. The ameliorative effects of SS and JF were less pronounced than those of JS. The contribution of biochar and SS-20 to the improvement of the soil quality index suggests additive effects with minimal interaction. Redundancy analysis identified EC and total potassium as the key environmental variables influencing microbial community structure at the phylum and genus levels, respectively. JS influenced the relative abundances of candidate lineages, such as Myxococcota, AG11, and Gemmatirosa, as well as functional genes associated with energy metabolism and cell motility. In summary, JS enhanced soil properties, modulated differentially abundant taxa and their metabolic potential, and consequently facilitated pakchoi production in saline–alkali soil. This study offers practical insights for the ecological management of saline–alkali farmland.