Influence of Decomposed Stubble Return on the Soil Microbial Community Under Perennial Crop Rotation

Abstract

The aim of this study was to understand how the application of decomposed stubble return (DSR), a type of bio-organic fertilization, affects soil microbial communities under crop rotation. The changes in microbial composition and diversity related to DSR were investigated based on metagenomic sequencing and comparative analysis of two groups of soil samples after a 3-year tomato-pepper-papaya rotation: the DSR and no-DSR (i.e., without DSR) groups, with the soils before crop rotation as the control group. Inter-group comparisons of the crop performance (growth and yield) and physicochemical soil properties (pH value, nutrient elements, and heavy metals) were also conducted to reveal the effects of DSR application on the soil. The relative abundance of bacteria was higher than 90% in all soil samples. Proteobacteria and Actinobacteria in the DSR group and Proteobacteria and Firmicutes in the no-DSR group, whereas Acidobacteria and Proteobacteria in the control, were the two most abundant phyla. The abundance of Proteobacteria decreased, whereas that of Actinobacteria increased, in the DSR-amended soil compared to the no-DSR soil. At genus level, Acidobacterium dominated in the control and genera Pseudomonas, Burkholderia, and Bacillus in the no-DSR group, while Burkholderia, Pseudomonas, and Bacillus in the DSR-amended soil comprised the majority of their microbiomes. The DSR soil had higher microbial diversity and relative abundance of Ascomycota fungi than the no-DSR group after the crop rotation. Along with higher diversity of microbial community, more favorable soil pH, better crop growth, higher crop yields, higher abundance of soil nutrient elements, and lower accumulation of heavy metals in the soil were found in the DSR group compared to the no-DSR one. Furthermore, the DSR soil had more similarities with the control than with the No-DSR soil, in aspects of microbial composition and microbe-derived potential gene functions. It was indicated that decomposed stubble return may improve soil conditions or prevent them from degradation incurred by long-term crop cultivation. It was suggested that the application of the compost derived from fermented post-harvest plant residue may be a general strategy for developing more sustainable agricultural systems.