Soil microbial diversity is believed to be vital in maintaining soil quality and health. Limited knowledge exists on the impact of cropping systems (mono-cropping and crop rotation) on the diversity of the whole soil microbiome. In this study, we investigated the effects of two cropping systems, namely crop rotation and mono-cropping, on the community structure and diversity of rhizosphere microbiome in the rhizosphere and bulk soil associated with maize plant using shotgun metagenomics. Whole DNA was extracted from bulk, and rhizosphere soils associated with maize plant from the mono-cropping (LT and LTc) and crop rotation (VD and VDc) sites, respectively, and sequenced employing shotgun metagenomics. The results obtained via the Subsystem database showed 23 bacteria, 2 fungi, and 3 archaea most abundant phyla. The major bacterial phyla are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Cyanobacteria, Spirochaetes, Aquificae, Verrucomicrobia, Chloroflexi, Planctomycetes, and Chlorobi. The major fungi phyla observed were Ascomycota and Basidiomycota, while the dominant archaea phyla are Euryarchaeota, Thaumarchaeota, and Crenarchaeota. Our diversity assessment showed that the rhizosphere microbial community was more abundant in the samples from the rotational crop site following VD>VDc>LT>LTc. Alpha diversity showed that there was no significant difference (P>0.05) in the soil microbial communities (P>0.05), while better diversity indicated that a significant difference (P = 0.01) occurred. Taken together, crop rotational practice was found to positively influence the rhizosphere microbial community associated with the maize plant.

土壤微生物多样性被认为对维持土壤质量和健康至关重要。关于种植系统（单一种植和轮作）对整个土壤微生物群落多样性的影响的知识有限。在这项研究中，我们使用鸟枪宏基因组学研究了两种作物系统，即轮作和单一作物，对与玉米植物相关的根际和大块土壤中根际微生物群落结构和多样性的影响。分别从单一作物（LT 和 LTc）和轮作（VD 和 VDc）位点的大块和与玉米植物相关的根际土壤中提取整个 DNA，并使用鸟枪宏基因组学进行测序。通过子系统数据库获得的结果显示 23 种细菌、2 种真菌和 3 种古细菌最丰富的门。主要的细菌门是厚壁菌门，拟杆菌，放线菌，变形菌，芽单胞菌门，酸杆菌门，蓝藻，螺旋体，产水菌门，疣微菌门，绿弯菌门，浮霉菌门，和Chlorobi。观察到的主要真菌门是子囊菌门和担子菌门，而优势古菌门是Euryarchaeota、Thaumarchaeota和Crenarchaeota 。. 我们的多样性评估表明，在 VD>VDc>LT>LTc 后轮作种植地的样品中，根际微生物群落更丰富。α多样性表明土壤微生物群落没有显着差异（P > 0.05）（P > 0.05），而更好的多样性表明发生了显着差异（P = 0.01）。总之，发现作物轮作实践对与玉米植物相关的根际微生物群落产生积极影响。