Clinical Pharmacist and Master’s student in Clinical Pharmacy with research interests in pharmacovigilance, behavioral interventions in mental health, and AI applications in clinical decision support. Experience includes digital health research with Bloomsbury Health (London) and pharmacovigilance practice in patient support programs. Published work covers drug awareness among healthcare providers, postpartum depression management, and patient safety reporting. 
Clinical Pharmacist and Master’s student in Clinical Pharmacy with research interests in pharmacovigilance, behavioral interventions in mental health, and AI applications in clinical decision support. Experience includes digital health research with Bloomsbury Health (London) and pharmacovigilance practice in patient support programs. Published work covers drug awareness among healthcare providers, postpartum depression management, and patient safety reporting. What was studied?
The study examines cadmium (Cd) accumulation in rice, a critical issue for food safety and heavy metal certification. It explores microbial mechanisms underlying Cd uptake differences between two cultivars—XS14 (low-Cd accumulator) and YY17 (higher-Cd accumulator), under varying soil amendments. Using high-throughput metagenomic sequencing and random forest models, the authors analyzed the structure, assembly, and function of root-associated microbiomes across bulk soil, rhizosphere, rhizoplane, and endosphere niches. The study sought to clarify how microbial communities shape varietal Cd uptake and to identify microbial taxa or genetic biomarkers predictive of accumulation capacity, thereby informing agricultural practices and supporting heavy metal certification programs.
Who was studied?
The primary subjects of this research were two rice cultivars: XS14, a conventional japonica rice identified as a low-Cd accumulator, and YY17, a widely used hybrid japonica rice known to accumulate higher levels of Cd. Both cultivars were grown in the same field site in Zhejiang province, China, in soils subject to varying amendments—lime, pig manure, biochar, commercial soil conditioner, and a control over six years. The field experiment was designed with randomized blocks and three replicates per treatment. Microbial communities were sampled from four plant-soil compartments (bulk soil, rhizosphere, rhizoplane, and endosphere) at harvest. In total, 120 DNA samples were analyzed for 16S rRNA amplicon sequencing to profile bacterial communities, while 12 representative samples (from control treatments) underwent shotgun metagenomic sequencing for functional and taxonomic analysis. Thus, the study encompasses not only the plants themselves but also the root-associated microbiomes occupying key ecological niches relevant to heavy metal uptake.
Most important findings
| Key Finding Category | Details and Significance |
|---|---|
| Cd Accumulation Differences | XS14 consistently accumulated significantly less Cd in grains than YY17, regardless of soil amendment, demonstrating its value as a low-Cd cultivar. The bioaccumulation factor was much lower for XS14, which is directly relevant for heavy metal certification programs focused on food safety. |
| Microbial Community Structure | Microbial community assembly and structure differed markedly between cultivars. XS14 exhibited more variable and functionally diverse microbiomes, with greater community dissimilarity across compartments and more robust, interconnected co-occurrence networks, especially in bulk soil and rhizosphere. This indicates a more adaptable and resilient microbiome, potentially contributing to reduced Cd uptake. |
| Assembly Mechanisms | Deterministic processes (host selection and environmental filtering) dominated assembly in both cultivars, but XS14 displayed higher stochasticity in the rhizosphere, suggesting increased adaptability to soil changes. |
| Taxonomic and Functional Biomarkers | Machine learning (random forest) identified key indicator taxa predictive of Cd accumulation capacity. XS14 was associated with Desulfobacteria (notably genus DP-20) enriched for sulfur cycling genes, while YY17 was associated with Nitrospiraceae (genus Nitrospira) enriched for nitrogen cycling genes. These taxa’s abundances correlated strongly with Cd levels in rice grains, supporting their use as biomarkers for certification or breeding programs. |
| Functional Gene Enrichment | XS14’s root microbiome was enriched for genes involved in sulfur cycling, amino acid and carbohydrate metabolism—functions linked to Cd immobilization and stress alleviation. In contrast, YY17’s microbiome had more nitrogen cycling genes. Metagenome-assembled genomes (MAGs) further supported these functional distinctions and revealed heavy metal resistance genes (e.g., Cd-exporting ATPases) in both cultivars’ microbiomes. |
| Implications for Certification | The identification of microbial and genetic biomarkers linked to Cd uptake provides actionable targets for monitoring or manipulating soil and rhizosphere microbiomes to support certification programs aiming to limit heavy metal content in rice grain. |
Key implications
The study’s findings have direct implications for heavy metal certification and food safety programs. Identifying microbial biomarkers such as Desulfobacteria and Nitrospira provides new tools for predicting and potentially manipulating Cd accumulation in rice. Incorporating such biomarkers into certification protocols could enhance risk assessment, guide the selection of rice varieties, and support the adoption of soil management practices that foster beneficial microbiota. These insights enable targeted interventions and monitoring strategies, strengthening regulatory frameworks and supporting the development of safer, certified rice products.
Citation
Cheng Z, Zheng Q, Shi J, He Y, Yang X, Huang X, Wu L, Xu J. Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars. ISME Communications. 2023;3(1):14. doi:10.1038/s43705-023-00213-z
Cadmium is a persistent heavy metal that accumulates in kidneys and bones. Dietary sources include cereals, cocoa, shellfish and vegetables, while smokers and industrial workers receive higher exposures. Studies link cadmium to kidney dysfunction, bone fractures and cancer.
