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. Overview
This systematic review critically examined 85 research articles published between 2005 and May 2020, focusing on the bioremediation potential of bacteria associated with the plant microbiome in soils contaminated by non-essential heavy metals, specifically arsenic, cadmium, and lead (Pb). The review targeted bacteria that not only inhabit plant-associated environments (rhizosphere or endophytes) but also exhibit plant growth-promoting (PGP) characteristics, express resistance to these heavy metals as measured by Minimum Inhibitory Concentration (MIC), and have well-characterized biochemical or molecular resistance mechanisms. The review utilized a PRISMA flowchart to select relevant studies and harmonized MIC units for comparative analysis. Researchers performed statistical analyses, including ANOVA and Tukey’s post hoc tests, to compare MIC values across metal types, bacterial genera, and growth media. They also conducted a qualitative analysis of resistance mechanisms and gene presence in reference genomes.
What was reviewed?
The review encompassed 424 bacterial species/strains spanning 62 genera, all associated with 50 distinct plant species. They selected bacteria for their dual capacity to promote plant growth and tolerate high concentrations of arsenic, cadmium, and lead. The studies they analyzed encompassed a global range of environments and included both rhizosphere and endophytic bacteria, with emphasis on species naturally occurring in plant-associated environments rather than those isolated from extreme or marine habitats. Researchers conducted in-depth molecular analyses on reference genomes from the most frequently studied genera, including Klebsiella, Enterobacter, Agrobacterium, Bacillus, Microbacterium, Pseudomonas, and Rhodococcus.
Most important Bacteria for Heavy Metal Remediation
The systematic review demonstrated that bacterial tolerance to heavy metals closely depends on both the identity of the metal and the bacterial genus. Across the analyzed genera, resistance to arsenic (particularly as arsenate) was generally higher and more widespread than resistance to cadmium and lead, which exhibited lower MIC values and thus were more toxic. Among the bacterial genera, Klebsiella and Enterobacter demonstrated the highest resistance to cadmium and lead, supported by robust biochemical (PGP traits like ACC deaminase, phosphate solubilization, and IAA production) and molecular (presence of cad and ars operon genes) mechanisms. Notably, the review identified significant variability in MIC values depending on the growth medium, especially for lead, highlighting the need for standardization in laboratory testing protocols.
The review further demonstrated that diverse “ars operon genes” (arsR, arsB, arsC, arsD, arsH, arsM), which were ubiquitous across the studied genera, primarily mediate arsenic resistance. Researchers identified cadmium resistance primarily with the cad operon (cadA, cadC, cadB, cadD) and the corresponding ATPase efflux pumps. Lead resistance, by contrast, remains less understood at the genetic level, with only a few reports of pbr operon genes, and none found in the main genera analyzed. Biochemical mechanisms such as siderophore production, nitrogen fixation, and antioxidant enzyme activity complement these molecular strategies, contributing to both metal detoxification and plant growth under heavy metal stress.
Key implications
For heavy metal certification programs such as HTMC, this review provides a robust scientific basis for selecting bacterial strains with proven efficacy in bioremediation and phytoremediation strategies for arsenic, cadmium, and lead-contaminated soils. The identification of Klebsiella and Enterobacter as leading candidates—owing to their high MICs and well-characterized resistance mechanisms—supports their prioritization in remediation consortia or bioaugmentation products. The findings underscore the necessity of standardized MIC testing protocols, as variations in media composition can significantly skew resistance assessments, particularly for lead. Furthermore, the review highlights that effective certification should consider not only the presence of resistance genes but also the demonstrated PGP traits, which are critical for the dual goals of environmental detoxification and crop productivity. Finally, the lack of detailed genetic understanding of lead resistance invites further research before certification of lead bioremediation claims.
Citation
González Henao S, Ghneim-Herrera T. Heavy Metals in Soils and the Remediation Potential of Bacteria Associated With the Plant Microbiome. Frontiers in Environmental Science. 2021;9:604216. doi:10.3389/fenvs.2021.604216
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.
Lead is a neurotoxic heavy metal with no safe exposure level. It contaminates food, consumer goods and drinking water, causing cognitive deficits, birth defects and cardiovascular disease. HMTC’s rigorous lead testing applies ALARA principles to protect infants and consumers and to prepare brands for tightening regulations.
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.
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.
