Comparative metagenomics on community structure and diversity of rhizomicrobiome associated with monoculture and soybean precedent carrot

Abstract

Several studies have explored the impact of cropping systems, including monoculture and crop rotation, on the plant rhizosphere - an essential dynamic in designing strategies for optimizing soil health and crop productivity. It remains largely unknown how these agricultural practices drive the diversity and community structure of the microbiome in the carrot rhizosphere. Thus, this study aims to profile the core rhizo-microbiome of carrots grown under a monoculture system and those grown after soybean cultivation. The microbial DNA extracted from 12 soil samples collected from monoculture carrot rhizosphere (MCR), soybean-precedent carrot rhizosphere (SCR), and uncultivated land (bulk soils) (BS) were analyzed via shotgun metagenomics sequencing. Findings show that bacterial phyla were the most dominant taxa across the sampling points. Principal Component Analysis (PCA) revealed that Pseudomonadota, Bacillota, and Actinomycetota are significantly enriched in soybean-precedent carrot rhizosphere, monoculture carrot rhizosphere, and bulk soil, respectively. Furthermore, genera Bradyrhizobium and Agromyces were significantly enriched, and Rhodococcus was exclusively present in soybean-precedent carrot rhizosphere. Alpha and Beta diversity analyses indicated that the microbial community composition was unique within and between the sampling sites (genus level). Redundancy Analysis (RDA) demonstrated that soil properties like silt (contributing 84.2%), total nitrogen (contributing 83.2%), organic carbon (contributing 81.0%), and sand texture (contributing 75.8%) explained the variance in microbiome composition. This study provides fundamental insight into how cropping systems influence carrot rhizo-microbiome. Crop rotation practice with soybeans was found to increase microbial composition and diversity in carrot plantations.

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