In-depth insights into carbohydrate-active enzyme genes regarding the disparities in soil organic carbon after 12-year rotational cropping system field study

Carbohydrate-active enzymes (CAZymes) play a crucial role in plant-derived carbon utilization and decomposition and are influenced by the crop rotation system; however, our knowledge of how different agricultural systems impact CAZyme functionality is still limited. We conducted a metagenomic analysis to evaluate the functional genes of CAZymes in a 12-year in situ farmland with three commonly used crop rotation systems: wheat-maize rotation (WM), wheat-cotton rotation (WC), and wheat-soybean rotation (WS). We aimed to study the impact of long-term use of crop rotation, especially crop rotation involving soybean, on soil organic carbon (SOC) content and to gain an in-depth understanding of the CAZyme genes in context of the disparities in SOC. After 12 years, the SOC content was significantly higher in WS than in WC (5.44 %) and WM (17.6 %). Furthermore, the crop rotation system had a significant effect on the soil microbial communities and CAZyme function genes. Detailly, WS increased the phyla abundance of Proteobacteria, Actinobacteria, and Firmicutes and enriched the glycoside hydrolase (GH) and carbohydrate-binding modules (CBM) genes; WC increased the abundance of Acidobacteria and Bacteroidota and enriched the polysaccharide lyase gene; WM increased the abundance of Nitrospirae, Candidatus_Rokubacteria, Chloroflexi and Gemmatimonadetes and enriched the gene abundance of glycosyltransferases and auxiliary activity genes. Additionally, Acidobacteria, Proteobacteria, and Actinobacteria are key phyla involved in soil carbon cycling and collectively contribute >70 % of the total CAZyme functional genes, which highlights their importance. In addition, our results indicated that total nitrogen content played a major role in influencing genes related to CAZymes, especially those belonging to the GH family. Our study demonstrates that WS conferred the advantage of increasing SOC across the three crop rotation systems. CAZyme analysis revealed that WS's could potentially support the increased abundance of Proteobacteria, Actinobacteria and Firmicutes in the soil community, at the same time potentially leading to increased number of GH and CBM genes in the soil, which may bolster the decomposition and transformation of plant-derived carbon, thus promoting an increase in SOC content. The findings of this study offer new insights into the microbial factors contributing to SOC enhancement in rotation systems.