Pakchoi Antioxidant Improvement and Differential Rhizobacterial Community Composition under Organic Fertilization

Field-based evidence for the enrichment of intrinsic antibiotic resistome stimulated by plant-derived fertilizer in agricultural soil

Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils. However, little is known about the effects of plant-derived fertilizer on soil antibiotic resistome. Herein, metagenomic sequencing was used to investigate the effects of a plant-derived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes (ARGs) in a soybean field along crop growth stages. ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure. The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly (P < 0.05) elevated at the sprout stage, to a level comparable to that in the manured soils. Whereas, unlike chicken manure mainly introducing manure-borne ARGs to soil, the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria. ARGs with abundances in amended soils significantly (P < 0.05) higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs. Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest. Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer, while in manured soils were Firmicutes and Actinobacteria. As revealed by multivariate statistical analyses, variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients, which was different from the failed establishment of manure-borne bacteria in the manured soils. Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome, and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.

Bioorganic fertilizer promotes pakchoi growth and shapes the soil microbial structure

As a functional probiotic, Bacillus subtilis can promote crop growth and improve nutrient utilization by various mechanisms, so it has been made into bioorganic fertilizer as a replacement for chemical fertilizer. However, the effects of B. subtilis bioorganic fertilizer application on the yield and quality of commercial crops of Brassica chinensis L., the soil physicochemical properties and the microflora have not been clarified. In this study, pot experiments were conducted using Brassica chinensis L. plants with four fertilization treatments: control without fertilization (CK), chemical fertilizer (CF), organic fertilizer (OF), and bioorganic fertilizer containing B. subtilis (BF). After 30 days of pot experiment, the results showed that BF efficiently improved plant height and biomass (1.20- and 1.93-fold, respectively); as well as significantly increasing soil available potassium and pH value. Using high-throughput sequencing, we examined the bacterial and fungal communities in the soil, and found that their diversity was remarkablely reduced in the BF treatment compared to CK group. A principal coordinate analysis also showed a clear separation of bacterial and fungal communities in the BF and CK groups. After application of B. subtilis bioorganic fertilizer, some beneficial bacteria (such as Bacillus and Ammoniphilus) and fungi (Trichoderma and Mortierella) were enriched. A network analysis indicated that bacteria were the dominant soil microbes and the presence of B. subtilis stimulated the colonization of beneficial microbial communities. In addition, predictive functional profiling demonstrated that the application of bioorganic fertilizer enhanced the function of mineral element metabolism and absorption and increased the relative abundance of saprotrophs. Overall, the application of bioorganic fertilizer effectively changed the soil microflora, improved the soil available potassium and pH value, and boosted the yield of Brassica chinensis L. This work has valuable implications for promoting the safe planting of facility vegetables and the sustainable development of green agriculture.