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 reviewed?
This review article provides a comprehensive synthesis of how omics technologies, namely metagenomics, metatranscriptomics, metaproteomics, and metabolomics, are advancing our understanding of heavy metal (HM) stress alleviation in soils and plants via the soil and plant-associated microbiome. The review addresses the global challenge of heavy metal contamination, highlighting the ecological and health impacts, and emphasizing the urgent need for effective remediation strategies to ensure food safety and environmental sustainability. The authors focus on microbe-mediated bioremediation, particularly the role of HM-tolerant microbial communities in the rhizosphere and endosphere of plants, and how omics techniques are enabling rapid identification, functional characterization, and exploitation of these communities for HM detoxification. The article details recent advances in the application of omics for profiling microbial diversity, mining resistance genes, elucidating biochemical pathways involved in HM tolerance, and integrating this knowledge into crop improvement and phytoremediation strategies.
Who was reviewed?
The review collates and critically examines research involving diverse plant species ranging from hyperaccumulators like Arabidopsis halleri and Azolla filiculoides to economically important crops such as rice, wheat, maize, and alfalfa that are exposed to various heavy metals, including cadmium, arsenic, lead, copper, zinc, mercury, and nickel. It synthesizes findings from studies targeting the associated microbial communities (bacteria, fungi, and archaea) residing in rhizosphere, endosphere, and phyllosphere environments. The article draws from experimental work using both culture-dependent and culture-independent (omics-based) approaches across multiple contaminated environments worldwide. Thus, the “who” encompasses both the plant holobionts under HM stress and their associated, often uncultivable, microbial populations, with an emphasis on those exhibiting HM resistance or bioremediation potential as revealed by omics investigations.
Most important findings
| Domain | Key Findings |
|---|---|
| Role of Microbiome | Plant-associated microbiota, especially from HM-contaminated environments, harbor diverse HM-tolerant species that enhance plant resilience and bioremediation efficiency through multiple mechanisms (e.g., biosorption, chelation, efflux, phytohormone production). |
| Omics Technologies | Omics approaches (metagenomics, metatranscriptomics, metaproteomics, metabolomics) enable identification of unculturable, HM-tolerant microbes, resistance genes (e.g., czcA, czcD, mer operon), and metabolic pathways involved in HM detoxification and plant-microbe interactions. |
| Functional Insights | Shotgun metagenomics and targeted amplicon sequencing allow profiling of community structure and resistome analysis; metatranscriptomics and metaproteomics reveal active genes/proteins under HM stress; metabolomics links microbial activity to changes in plant and soil metabolites. |
| Bioremediation Enhancement | Omics techniques face technical barriers (e.g., sample complexity, data analysis load, metabolite diversity). The field-scale application of microbial inoculants is hindered by their limited adaptation and persistence in natural environments. Innovations in culture methods and extraction protocols are needed. |
| Translation to Practice | Knowledge of HM-tolerant microbiota and genes can be integrated into plant breeding programs (holobiont breeding) and bioremediation protocols, supporting the development of crops suitable for contaminated soils and more robust heavy metal certification standards. |
| Limitations & Future Directions | Omics techniques face technical barriers (e.g., sample complexity, data analysis load, metabolite diversity). Field-scale application of microbial inoculants is challenged by their adaptation and persistence in natural environments. Innovations in culture methods and extraction protocols are needed. |
Key implications
The review demonstrates that integrating omics analysis into heavy metal management enables the identification and deployment of HM-tolerant microbial communities and genes for bioremediation and crop improvement. This knowledge can be leveraged by heavy metal certification programs to establish science-based safety standards, validate the efficacy of bioremediation, and support evidence-based regulatory decisions. Omics-guided strategies facilitate the transition from empirical to precision remediation and certification, enhancing food safety and environmental protection in line with sustainable agriculture and public health goals.
Citation
Phurailatpam L, Dalal VK, Singh N, Mishra S. Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome. Frontiers in Sustainable Food Systems. 2022;5:817932. doi:10.3389/fsufs.2021.817932
Heavy metals are high-density elements that accumulate in the body and environment, disrupting biological processes. Lead, cadmium, arsenic, mercury, nickel, tin, aluminum, and chromium are of greatest concern due to persistence, bioaccumulation, and health risks, making them central to the HMTC program’s safety standards.
Heavy metals are high-density elements that accumulate in the body and environment, disrupting biological processes. Lead, cadmium, arsenic, mercury, nickel, tin, aluminum, and chromium are of greatest concern due to persistence, bioaccumulation, and health risks, making them central to the HMTC program’s safety standards.
