Bio-alchemy: a review of bacterial mechanisms for heavy metal sequestration, transformation, and bioremediation

Michael Josh Ramirez , Iza Clare Mira , Dyanne Jasmine Rafael , Vincent Chuabio , Bernadette Bagon , Jubert Marquez

Systems Microbiology and Biomanufacturing ›› 2026, Vol. 6 ›› Issue (6) : 154

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Systems Microbiology and Biomanufacturing ›› 2026, Vol. 6 ›› Issue (6) :154 DOI: 10.1007/s43393-026-00557-2
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Bio-alchemy: a review of bacterial mechanisms for heavy metal sequestration, transformation, and bioremediation
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Abstract

Heavy metal contamination has become a growing concern due to rapid industrialization. Contaminants from sources such as wastewater, mining sites, and harmful agricultural chemicals have different transfer mechanisms that directly threaten ecosystems and living organisms. Current management practices employed are limited in terms of long-term sustainability and efficiency. Bacterial bioremediation has therefore emerged as a promising biological strategy for the removal, sequestration, immobilization, and transformation of heavy metals in contaminated environments. This review explores current knowledge of the biosorptive and bioaccumulative capabilities of various bacterial strains, including Bacillus, Pseudomonas, Enterobacter, Streptomyces, and Escherichia, and highlights their mechanisms of resistance, sequestration, and metal transformation. Aside from this, it also synthesizes their real-world applications in wastewater treatment, soil rehabilitation, agricultural biofertilization, and environmental monitoring. The review also discusses emerging approaches involving bacterial consortia, omics-based analyses, computational tools, and engineered remediation systems. While bacterial strategies have significant potential for eliminating and remediating heavy metals, there are still challenges related to their sensitivity to physicochemical conditions and the potential for metal re-release. Addressing these limitations will require a better understanding of strain-specific mechanisms, microbial interactions, environmental conditions, and the long-term stability of remediation systems. Overall, bacterial bioremediation offers a versatile and potentially sustainable approach to managing persistent heavy metal contamination.

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Bacterial bioremediation / Biosorption / Bioaccumulation / Detoxification / Heavy metal contamination

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Michael Josh Ramirez, Iza Clare Mira, Dyanne Jasmine Rafael, Vincent Chuabio, Bernadette Bagon, Jubert Marquez. Bio-alchemy: a review of bacterial mechanisms for heavy metal sequestration, transformation, and bioremediation. Systems Microbiology and Biomanufacturing, 2026, 6 (6) : 154 DOI:10.1007/s43393-026-00557-2

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References

[1]

Ahamad MI, Yao Z, Ren L, Zhang C, Li T, Lu H, Mehmood MS, Rehman A, Adil M, Lu S, Feng W. Impact of heavy metals on aquatic life and human health: a case study of River Ravi Pakistan. Front Mar Sci, 2024.

[2]

An Q, Deng S, Xu J, Nan H, Li Z, Song J-L. Simultaneous reduction of nitrate and Cr(VI) by Pseudomonas aeruginosa strain G12 in wastewater. Ecotoxicol Environ Saf, 2020, 191: 110001.

[3]

Arora R. Adsorption of heavy metals–a review. Mater Today: Proc 9th Int Conf Mater Process Charact ICMPC-2019, 2019, 18: 4745-50.

[4]

Arunakumara KKIU, Walpola BC, Yoon M-H. Current status of heavy metal contamination in Asia’s rice lands. Rev Environ Sci Bio/Technol, 2013, 12435577.

[5]

Aryal M. A comprehensive study on the bacterial biosorption of heavy metals: materials, performances, mechanisms, and mathematical modellings. Rev Chem Eng, 2021, 37671554.

[6]

Aslam A, Kanwal F, Javied S, Nisar N, Torriero AAJ. Microbial biosorption: a sustainable approach for metal removal and environmental remediation. Int J Environ Sci Technol, 2025, 22131324576.

[7]

Awasthi G, Chester A, Chaturvedi R, Prakash J. Study on role of pseudomonas aeruginosa on heavy metal bioremediation. 2015.

[8]

Ayach J, El Malti W, Duma L, Lalevée J, Al Ajami M, Hamad H, Hijazi A. Comparing conventional and advanced approaches for heavy metal removal in wastewater treatment: an in-depth review emphasizing filter-based strategies. Polymers, 2024, 16141959.

[9]

Banerjee G, Pandey S, Ray AK, Kumar R. Bioremediation of heavy metals by a novel bacterial strain enterobacter cloacae and its antioxidant enzyme activity, flocculant production, and protein expression in presence of lead, cadmium, and nickel. Water Air Soil Pollut, 2015, 226491.

[10]

Blindauer CA. Bacterial metallothioneins: past, present, and questions for the future. J Biol Inorg Chem, 2011, 167101124.

[11]

Briffa J, Sinagra E, Blundell R. Heavy metal pollution in the environment and their toxicological effects on humans. Heliyon, 2020.

[12]

Cai X, Zheng X, Zhang D, Iqbal W, Liu C, Yang B, Zhao X, Lu X, Mao Y. Microbial characterization of heavy metal resistant bacterial strains isolated from an electroplating wastewater treatment plant. Ecotoxicol Environ Saf, 2019, 181: 472-80.

[13]

Cerasi M, Liu JZ, Ammendola S, Poe AJ, Petrarca P, Pesciaroli M, Pasquali P, Raffatellu M, Battistoni A. The ZupT transporter plays an important role in zinc homeostasis and contributes to Salmonella enterica virulence. Metallomics, 2014, 6484553.

[14]

Cerrillo-Gonzalez MdelM, Villen-Guzman M, Rodriguez-Maroto JM, Paz-Garcia JM. Metal recovery from wastewater using electrodialysis separation. Metals, 2024, 14138.

[15]

Chandrangsu P, Rensing C, Helmann JD. Metal homeostasis and resistance in bacteria. Nat Rev Microbiol, 2017, 15633850.

[16]

Charan K, Mandal J, Bhattacharyya P. Application of autochthonous extremophilic in remediation of groundwater—a sorption-based metal cleaning approach. Groundw Sustainable Dev, 2024, 24: 101063.

[17]

Deng S, Chen J, Chang J. Application of biochar as an innovative substrate in constructed wetlands/biofilters for wastewater treatment: performance and ecological benefits. J Clean Prod, 2021, 293: 126156.

[18]

Djedjibegovic J, Marjanovic A, Tahirovic D, Caklovica K, Turalic A, Lugusic A, Omeragic E, Sober M, Caklovica F. Heavy metals in commercial fish and seafood products and risk assessment in adult population in Bosnia and Herzegovina. Sci Rep, 2020, 10113238.

[19]

Dong Y, Zan J, Lin H. Bioleaching of heavy metals from metal tailings utilizing bacteria and fungi: mechanisms, strengthen measures, and development prospect. J Environ Manage, 2023, 344: 118511.

[20]

El Motaleb MMA, Sabbagh E, Din Mohamed SME, Wafy K. Biosorption of Cu2+, Pb2 + and Cd2 + from wastewater by dead biomass of <i>Streptomyces cyaneus</i> Kw42. Int J Curr Microbiol Appl Sci, 2020, 9142235.

[21]

El-Sharkawy M, Alotaibi MO, Li J, Du D, Mahmoud E. Heavy metal pollution in coastal environments: ecological implications and management strategies: a review. Sustainability, 2025, 172701.

[22]

Gao X, Meng X. Photocatalysis for heavy metal treatment: a review. Processes, 2021, 9101729.

[23]

Garg A, Chauhan P, Kaur C, Perveen S, Arora PK, Garg SK, Singh VP, Srivastava A. Bacterial bioremediation strategies for heavy metal detoxification: a multidisciplinary approach. Environ Sustain, 2025, 83395417.

[24]

Guo H, Luo S, Chen L, Xiao X, Xi Q, Wei W, Zeng G, Liu C, Wan Y, Chen J, He Y. Bioremediation of heavy metals by growing hyperaccumulaor endophytic bacterium Bacillus sp. L14. Bioresour Technol, 2010, 101228599605.

[25]

Haidar Z, Fatema K, Shoily SS, Sajib AA. Disease-associated metabolic pathways affected by heavy metals and metalloid. Toxicol Rep, 2023, 10: 554-70.

[26]

Halema AA, El-Beltagi HS, Al-Dossary O, Alsubaie B, Henawy AR, Rezk AA, Almutairi HH, Mohamed AA, Elarabi NI, Abdelhadi AA. Omics technology draws a comprehensive heavy metal resistance strategy in bacteria. World J Microbiol Biotechnol, 2024, 406193.

[27]

Hamdan AM, Abd-El-Mageed H, Ghanem N. Biological treatment of hazardous heavy metals by Streptomyces rochei ANH for sustainable water management in agriculture. Sci Rep, 2021, 1119314.

[28]

Hazaa M. Bioremediation of Zn + 2, Cu + 2 and Fe + 2 using Bacillus subtilis D215 and Pseudomonas putida biovar A D225. 2013.

[29]

Jhariya U, Chien M-F, Umetsu M, Kamitakahara M. New insights into immobilized bacterial systems for removal of heavy metals from wastewater. Int J Environ Sci Technol, 2025, 229831934.

[30]

Jiang J, Shi Y, Ma NL, Ye H, Verma M, Ng HS, Ge S. Utilizing adsorption of wood and its derivatives as an emerging strategy for the treatment of heavy metal-contaminated wastewater. Environ Pollut, 2024, 340: 122830.

[31]

Kang C-H, Kwon Y-J, So J-S. Bioremediation of heavy metals by using bacterial mixtures. Ecol Eng, 2016, 89: 64-9.

[32]

Karaouzas I, Kapetanaki N, Mentzafou A, Kanellopoulos TD, Skoulikidis N. Heavy metal contamination status in Greek surface waters: a review with application and evaluation of pollution indices. Chemosphere, 2021, 263: 128192.

[33]

Khan ZI, Muhammad FG, Ahmad K, Alrefaei AF, Ahmad T, Ejaz A, Nadeem M, Shahzadi M, Muqaddas H, Mehmood N. Evaluation of potential ecological risk assessment of toxic metal (lead) in contaminated meadows in the vicinity of suburban city: soil vs forages vs livestock. Braz J Biol, 2023, 83: e272087.

[34]

Kicinska A, Pomykala R, Izquierdo-Diaz M. Changes in soil pH and mobility of heavy metals in contaminated soils. 2021. https://doi.org/10.1111/ejss.13203

[35]

Kondakindi VR, Pabbati R, Erukulla P, Maddela NR, Prasad R. Bioremediation of heavy metals-contaminated sites by microbial extracellular polymeric substances—a critical view. Environ Chem Ecotoxicol, 2024, 6: 408-21.

[36]

Lata S, Sharma S, Kaur S. OMICS approaches in mitigating metal toxicity in comparison to conventional techniques used in cadmium bioremediation. Water Air Soil Pollut, 2023, 2343148.

[37]

Li X, Islam MM, Chen L, Wang L, Zheng X. Metagenomics-guided discovery of potential bacterial metallothionein genes from the soil microbiome that confer Cu and/or Cd resistance. Appl Environ Microbiol, 2020, 869e0290719.

[38]

Li X, Ren Z, Crabbe MJC, Wang L, Ma W. Genetic modifications of metallothionein enhance the tolerance and bioaccumulation of heavy metals in Escherichia coli. Ecotoxicol Environ Saf, 2021, 222: 112512.

[39]

Li D, Pan B, Wang Y, Han X, Lu Y. Bioaccumulation and health risks of multiple trace metals in fish species from the heavily sediment-laden Yellow River. Mar Pollut Bull, 2023, 188: 114664.

[40]

Li H, Cui X, Sun Y, Zheng P, Wang L, Shi X. Advances in microbial remediation of heavy metal-contaminated soils: mechanisms, synergistic technologies, field applications and future perspectives. Toxics, 2025, 13121069.

[41]

Luka Y, Highina BK, Zubairu A, Adeleke AJ, Hamadou M, Musti YA, Abubakar AM, Yunus MU. Biosorption as technique for remediation of heavy metals from wastewater using microbial biosorbent. Biol Sci, 2024, 4156474.

[42]

Magahud J, Sanchez P, Badayos R, Sta. Cruz P. Levels and potential sources of heavy metals in major irrigated rice areas of the Philippines. IAMURE Int J Ecol Conserv, 2015, 15111

[43]

Malik G, Arora R, Chaturvedi R, Paul MS. Implementation of genetic engineering and novel omics approaches to enhance bioremediation: a focused review. Bull Environ Contam Toxicol, 2022, 108344350.

[44]

Malviya A, Jaspal D. (2023). Biosorption application in water reuse and recovery. In: Resource recovery in drinking water treatment (pp. 93–105). Elsevier. https://doi.org/10.1016/B978-0-323-99344-9.00007-4

[45]

Mathivanan K, Chandirika JU, Vinothkanna A, Yin H, Liu X, Meng D. Bacterial adaptive strategies to cope with metal toxicity in the contaminated environment—a review. Ecotoxicol Environ Saf, 2021, 226: 112863.

[46]

Miclean M, Cadar O, Levei EA, Roman R, Ozunu A, Levei L. Metal (Pb, Cu, Cd, and Zn) transfer along food chain and health risk assessment through raw milk consumption from free-range cows. Int J Environ Res Public Health, 2019, 16214064.

[47]

Mishra S, Bharagava RN, More N, Yadav A, Zainith S, Mani S, Chowdhary P. Sobti RC, Arora NK, Kothari R. Heavy metal contamination: an alarming threat to environment and human health. Environmental biotechnology: for sustainable future, 2019Springer103125.

[48]

Mitchell K. What are the different soil types—And why does it matter?. 2023. https://www.lawnmoregainesville.com/blog/soil-types

[49]

Navarrete IA, Gabiana CC, Dumo JRE, Salmo SG, Guzman MALG, Valera NS, Espiritu EQ. Heavy metal concentrations in soils and vegetation in urban areas of Quezon City, Philippines. Environ Monit Assess, 2017, 1894145.

[50]

Nnaji ND, Onyeaka H, Miri T, Ugwa C. Bioaccumulation for heavy metal removal: a review. SN Appl Sci, 2023, 55125.

[51]

Nnaji ND, Anyanwu CU, Miri T, Onyeaka H. Mechanisms of heavy metal tolerance in bacteria: a review. Sustainability, 2024, 162411124.

[52]

Oladimeji TE, Oyedemi M, Emetere ME, Agboola O, Adeoye JB, Odunlami OA. Review on the impact of heavy metals from industrial wastewater effluent and removal technologies. Heliyon, 2024.

[53]

Pande V, Pandey SC, Sati D, Bhatt P, Samant M. Microbial interventions in bioremediation of heavy metal contaminants in agroecosystem. Front Microbiol, 2022.

[54]

Paul V, Sankar MS, Vattikuti S, Dash P, Arslan Z. Pollution assessment and land use land cover influence on trace metal distribution in sediments from five aquatic systems in southern USA. Chemosphere, 2021, 263: 128243.

[55]

Peijnenburg W. Bioavailability of heavy metals in soil a review of tools, models, and regulatory applications. 2025. https://www.maxapress.com/article/doi/https://doi.org/10.48130/ebp-0025-0011

[56]

Pham VHT, Kim J, Chang S, Chung W. Bacterial biosorbents, an efficient heavy metals green clean-up strategy: prospects, challenges, and opportunities. Microorganisms, 2022, 103610.

[57]

Quintelas C, Rocha Z, Silva B, Fonseca B, Figueiredo H, Tavares T. Biosorptive performance of an <i>Escherichia coli</i> biofilm supported on zeolite NaY for the removal of Cr(VI), Cd(II), Fe(III) and Ni(II). Chem Eng J, 2009, 15211105.

[58]

Ramya D, Thatheyus AJ. Microscopic investigations on the biosorption of heavy metals by bacterial cells: a review. Sci Int, 2018, 61117.

[59]

Rashid A, Schutte BJ, Ulery A, Deyholos MK, Sanogo S, Lehnhoff EA, Beck L. Heavy metal contamination in agricultural soil: environmental pollutants affecting crop health. Agronomy, 2023, 1361521.

[60]

Sharma P, Bano A, Singh SP, Dubey NK, Chandra R, Iqbal HMN. Recent advancements in microbial-assisted remediation strategies for toxic contaminants. Clean Chem Eng, 2022, 2: 100020.

[61]

Sharma P, Singh SP, Iqbal HMN, Tong YW. Omics approaches in bioremediation of environmental contaminants: an integrated approach for environmental safety and sustainability. Environ Res, 2022, 211: 113102.

[62]

Siddique AB, Helal A, Patindol AS, Lumanao TA, Longatang DM, Rahman KJG, Catalvas MA, Tulin LPA, Shaibur MR. Assessment of heavy metal contamination and ecological risk in urban river sediments: a case study from Leyte, Philippines. Pollutants, 2025, 517.

[63]

Sodhi KK, Mishra LC, Singh CK, Kumar M. Perspective on the heavy metal pollution and recent remediation strategies. Curr Res Microb Sci, 2022, 3: 100166.

[64]

Sonone S, Jadhav S, Sankhla MS, Kumar R. Water contamination by heavy metals and their toxic effect on aquaculture and human health through food chain. Lett Appl Nanobiosci, 2020, 102214866.

[65]

Sreedevi PR, Suresh K, Jiang G. Bacterial bioremediation of heavy metals in wastewater: a review of processes and applications. J Water Process Eng, 2022, 48: 102884.

[66]

Sun J, He X, Le Y, Al-Tohamy R, Ali SS. Potential applications of extremophilic bacteria in the bioremediation of extreme environments contaminated with heavy metals. J Environ Manage, 2024, 352: 120081.

[67]

Tanhan P, Lansubsakul N, Phaochoosak N, Sirinupong P, Yeesin P, Imsilp K. Human Health Risk Assessment of Heavy Metal Concentration in Seafood Collected from Pattani Bay. Thail Toxics, 2023, 11118.

[68]

Tchounwou PB, Yedjou CG, Patlolla AK, Sutton DJ. Luch A. Heavy metal toxicity and the environment. Molecular, clinical and environmental toxicology: volume 3: environmental toxicology, 2012Springer133164.

[69]

Thai TD, Lim W, Na D. Synthetic bacteria for the detection and bioremediation of heavy metals. Front Bioeng Biotechnol, 2023.

[70]

Vardhan KH, Kumar PS, Panda RC. A review on heavy metal pollution, toxicity and remedial measures: current trends and future perspectives. J Mol Liq, 2019, 290: 111197.

[71]

Wagh VM, Panaskar DB, Mukate SV, Gaikwad SK, Muley AA, Varade AM. Health risk assessment of heavy metal contamination in groundwater of Kadava River Basin, Nashik, India. Model Earth Syst Environ, 2018, 4396980.

[72]

Wan Y, Liu J, Zhuang Z, Wang Q, Li H. Heavy metals in agricultural soils: sources, influencing factors, and remediation strategies. Toxics, 2024, 12163.

[73]

Wang J. A review on the ecotoxicological effects of heavy metals on aquatic organisms-siftdesk. SDRP J Earth Sci Environ Stud, 2022.

[74]

Wróbel M, Śliwakowski W, Kowalczyk P, Kramkowski K, Dobrzyński J. Bioremediation of heavy metals by the genus bacillus. Int J Environ Res Public Health, 2023, 2064964.

[75]

Yan K, Wang H, Lan Z, Zhou J, Fu H, Wu L, Xu J. Heavy metal pollution in the soil of contaminated sites in China: research status and pollution assessment over the past two decades. J Clean Prod, 2022, 373: 133780.

[76]

Yang R, Roshani D, Gao B, Li P, Shang N. Metallothionein: a comprehensive review of its classification, structure, biological functions, and applications. Antioxidants, 2024, 137825.

[77]

Yin S, Zhang X, Yin H, Zhang X. Current knowledge on molecular mechanisms of microorganism-mediated bioremediation for arsenic contamination: a review. Microbiol Res, 2022, 258: 126990.

[78]

Zakaria Z, Zulkafflee NS, Redzuan M, Selamat NA, Ismail J, Praveena MR, Tóth SM, Razis A. Understanding potential heavy metal contamination, absorption, translocation and accumulation in rice and human health risks. Plants, 2021, 1061070.

[79]

Zamora-Ledezma C, Negrete-Bolagay D, Figueroa F, Zamora-Ledezma E, Ni M, Alexis F, Guerrero VH. Heavy metal water pollution: a fresh look about hazards, novel and conventional remediation methods. Environ Technol Innov, 2021, 22: 101504.

[80]

Zhang Z, Zhao Y, Wei T, Bai X, Chen Z, Lei X, Liu Y. Constructed wetlands for metallic wastewater treatment: an updated global profile. J Water Process Eng, 2024, 65: 105852.

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