Unveiling the Sustainable and Biological Remediation of Heavy Metals Contaminations in Soils and Water Ecosystems Through Potential Microbes—A Review

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This paper focus the topical field of heavy metals bio-remediation and comprehensive review the challenge of heavy metals contaminants, remediation strategy development, potential mechanisms and proposed future development direction. This review summarizes valuable information, which is helpful for understanding and promoting strategies for  heavy metals control through microbial strategy. However, before it can be published, the following issues should be addressed.

1. The figures are not mentioned in main text.
2. Section 2: I think authors should include the contaminated situation of HM with at least some representative data.
3. Section 2.4: I think there should be some HM concentration data in foods to emphasize the food safety concern.
4. Line 180: Maybe a strict policy is more appropriate here to emphasize the concern.
5. Line 213-215: It is better to detail the function of AOPs in the HM removal process
6. Line 216: I don’t think the word “degrade”is rigorous enough for HM.
7. Section 3: The HM removal methods should be reorganized more logically, i suggest to divide them as physical, chemical and biological, while the nano-remediation can be included in the physical-chemical interdisciplinary approach. And authors should conclude the advantages and disadvantages of these methods to show the important of microbial  remediation.
8. Figure 3: You describe the plant system in bioremediation, however, you didn’t make a in-depth statement on microbial and plant systems. Why we should focus on the microbial strategy? I suggest authors to reorganize the text from line 252-270.
9. Figure 3:Remove the white background of the“Fungi”?
10. The writing for heavy metals in the text is not uniform. Sometimes it is written as "HM", sometimes as "HMs", and sometimes it is not abbreviated.
11. Line 288:I think it would be better to insert a brief introduction about fungi here to correspond with the two parts above and below.
12. Table 1, “Algae” section, line 11:  revise AARLG074 to “SP. AARLG074”.
13. Please check whether the position of Table 1 in the manuscript is appropriate.
14. The manuscript lacks sufficient discussion on microbial functional enzymes. Please verify whether the abstract accurately reflects the paper's scope, as this aspect appears underrepresented.

Author Response

Reply to Reviewer 1

This paper focus the topical field of heavy metals bio-remediation and comprehensive review the challenge of heavy metals contaminants, remediation strategy development, potential mechanisms and proposed future development direction. This review summarizes valuable information, which is helpful for understanding and promoting strategies for heavy metals control through microbial strategy. However, before it can be published, the following issues should be addressed.

Author response: Thank you so much for your comments and we really appreciate your concerns for the improvement of our manuscript.

 

1#The figures are not mentioned in main text.

Author response: Thank you for pointing out the mistakes. We have included Figure 1a and 1b in the main text.

Revised and mentiond as (Figure 1a) and (Figure 1b) with red font highlights.

2#Section 2: I think authors should include the contaminated situation of HM with at least some representative data.

Author response: Thank you for your valuable comment. Representative data on heavy metal contamination in soil, water, and food have been incorporated into Section 2 to better illustrate the extent and severity of the issue.

Revised as section 2 heading:

Heavy metal contamination has been identified as a growing global concern, with estimates indicating that approximately 14% to 17% of the world’s arable land is contaminated by at least one heavy metal, translating to nearly 242 million hectares of affected land (https://doi.org/10.1039/d4ra04639k). This widespread contamination poses substantial risks to agricultural productivity and public health. It has been estimated that between 900 million and 1.4 billion people reside in regions classified as high-risk zones for heavy metal exposure. In one study, Lake Maurepas exhibited alarmingly high concentrations of heavy metals and nutrients, with arsenic levels reaching up to 420% above the acceptable limit for lakes and 6,300% over the EPA's threshold for drinking water (https://doi.org/10.3390/environments11120268). Additionally, lead and cadmium were detected at concentrations substantially exceeding safe limits, while nickel, copper, and manganese were also observed above environmental safety thresholds. In urban soil studies, lead (95.8 mg/kg) and barium (86.8 mg/kg) emerged as the most prevalent contaminants (https://doi.org/10.3390/ijerph19031105). Moderate levels of chromium (13.8 mg/kg) and arsenic (5.14 mg/kg) were also reported, with selenium, cadmium, and silver detected at lower concentrations (below 1 mg/kg) (https://doi.org/10.3390/ijerph19031105). Elevated levels of copper, nickel, and zinc were particularly noted in the Lower Mississippi River Valley, which also exhibited moderate to high concentrations of cadmium, chromium, lead, nickel, and iron. Similarly, the River Swat demonstrated elevated concentrations of arsenic. In certain soil samples, nickel concentrations reached up to 214.4 mg/kg, surpassing international soil quality standards, and were attributed primarily to geogenic sources (https://doi.org/10.1016/j.fct.2010.07.018).

 

3#Section 2.4: I think there should be some HM concentration data in foods to emphasize the food safety concern.

Author response: Thank you for the helpful suggestion. Representative heavy metal concentration data in various food items have been added to highlight the associated food safety concerns.

Revised:

Elevated concentrations of heavy metals have been detected in various food items, raising significant concerns regarding food safety and human health. Studies have reported cadmium levels in rice exceeding 0.4 mg/kg, surpassing the maximum permissible limits set by international food safety authorities (https://link.springer.com/article/10.1007/s11356-020-11902-w). Lead concentrations in vegetables have been found up to 2.1 mg/kg, while mercury levels in certain fish species have reached 0.8 mg/kg, both exceeding recommended dietary thresholds (https://doi.org/10.1016/j.jes.2019.02.018). The chronic intake of such contaminated food has been associated with bioaccumulation and potential toxic effects, highlighting the urgent need for monitoring and regulatory control.

 

4#Line 180: Maybe a strict policy is more appropriate here to emphasize the concern.

Author response: Thank you for the suggestion. The sentence has been revised to emphasize the need for stricter policy measures to highlight the seriousness of heavy metal contamination and its associated risks.

Revised: Line(s) as below:

Given the widespread occurrence and persistence of heavy metal contamination in environmental and food matrices, the implementation of stricter regulatory policies is warranted to mitigate associated risks. Such policies would enhance monitoring, limit permissible exposure levels, and promote safer agricultural and industrial practices. A more rigorous framework is essential to address the long-term implications for ecosystem integrity and public health.

 

5#Line 213-215: It is better to detail the function of AOPs in the HM removal process

Author response: Thank you for your valuable suggestion. In response, we have expanded the discussion to provide more detail on the function of Advanced Oxidation Processes (AOPs) in the heavy metal (HM) removal process. Specifically, we have clarified that AOPs contribute to HM remediation primarily through oxidation-induced transformations, including the conversion of metal ions to less soluble or less toxic forms, facilitation of co-precipitation, and breakdown of metal-organic complexes

Revised as: Advanced Oxidation Processes (AOPs) play a crucial role in the removal of heavy metals through the generation of highly reactive species, primarily hydroxyl (^•OH) and sulfate (SO₄^•⁻) radicals (10.1016/j.jhazmat.2024.135449). These reactive intermediates facilitate the oxidation of metal ions, transformation into less toxic or more stable forms, and in some cases, precipitation as insoluble hydroxides or oxides. Furthermore, AOPs can enhance the breakdown of complexed metal-organic species, thereby improving overall removal efficiency in contaminated water and soil systems.

 

6#Line 216: I don’t think the word “degrade”is rigorous enough for HM.

Author response: Thank you for your observation. We agree that the term “degrade” is not appropriate in the context of heavy metals, as they are elemental and cannot be degraded. Accordingly, the word “degrade” has been replaced with “remove” to ensure scientific accuracy and clarity.

7#Section 3: The HM removal methods should be reorganized more logically, I suggest to divide them as physical, chemical and biological, while the nano-remediation can be included in the physical-chemical interdisciplinary approach. And authors should conclude the advantages and disadvantages of these methods to show the important of microbial remediation.

Author response: Thank you for the constructive suggestion. Section 3 has been reorganized by classifying the HM removal methods into physical, chemical, and biological categories, with nano-remediation discussed under the interdisciplinary physical–chemical approach, and a comparative summary of their advantages and disadvantages has been included to emphasize the significance of microbial remediation.

Revised Line(s) as:

Nano-remediation techniques, which often integrate surface adsorption, redox reactions, and catalytic functions, may be more appropriately classified under an interdisciplinary physical–chemical category. Each method presents distinct advantages and limitations. Physical methods such as filtration and adsorption are simple and rapid but may lack selectivity. Chemical treatments offer high efficiency but often involve secondary pollution and higher operational costs. Biological approaches, particularly microbial remediation, are eco-friendly and cost-effective, although they may require longer treatment times and are sensitive to environmental conditions. Highlighting these contrasts underscores the growing importance and potential of microbial strategies in sustainable heavy metal remediation.

 

 

8#Figure 3: You describe the plant system in bioremediation, however, you didn’t make a in-depth statement on microbial and plant systems. Why we should focus on the microbial strategy? I suggest authors to reorganize the text from line 252-270.

Author response: The spotted section has been revised. Please see the revised section 3

9#Figure 3: Remove the white background of the“Fungi”?

Author response: We have revised based on your concern and corrected it into our revised manuscript.

10#The writing for heavy metals in the text is not uniform. Sometimes it is written as "HM", sometimes as "HMs", and sometimes it is not abbreviated.

Author response: Revised “HMàHMs” throughout the manuscript.

 

11#Line 288: I think it would be better to insert a brief introduction about fungi here to correspond with the two parts above and below.

Author response: Revised as suggested.

12#Table 1, “Algae” section, line 11:  revise AARLG074 to “SP. AARLG074”.

Author response: Revised as suggested.

 

13#Please check whether the position of Table 1 in the manuscript is appropriate.

Author response: Revised and placed where appropriate.

14#The manuscript lacks sufficient discussion on microbial functional enzymes. Please verify whether the abstract accurately reflects the paper's scope, as this aspect appears underrepresented.

Abstract was well written for the and somewhere in the manuscript can be revised based on the - Explain more from -Cao et al., 2022; Molalign et al., 2020)

Author response: Thank you for this excellent insight. The suggested discussion and references has been added to the revised manuscript

Revised: Microbial functional enzymes play a pivotal role in pollutant biotransformation and detoxification. Enzymes such as laccases, dehydrogenases, monooxygenases, and reductases contribute to the degradation of hydrocarbons, dyes, plastics, and heavy metals, often within microbial consortia that facilitate cooperative metabolism and environmental adaptation (Cao et al., 2022; Tarekegn et al., 2020; Singh et al., 2020). These enzymatic systems are essential for bioavailability enhancement, redox reactions, and transformation of xenobiotic compounds into less toxic intermediates (Strong & Claus, 2011; Sharma et al., 2018). Therefore, the functional enzymatic profile of microbial communities should be considered a core element in designing effective bioremediation strategies.

 

Reference Added

1. Cao, Z.; Yan, W.; Ding, M.; Yuan, Y. Construction of microbial consortia for microbial degradation of complex compounds. Front. Bioeng. Biotechnol. 2022, 10, 1051233. (https://doi.org/10.3389/fbioe.2022.1051233).
2. Tarekegn, M.M.; Salilih, F.Z.; Ishetu, A.I. Microbes used as a tool for bioremediation of heavy metal from the environment. Cogent Food Agric. 2020, 6, 1783174. (https://doi.org/10.1080/23311932.2020.1783174).
3. Singh, R.; Kumar, M.; Mittal, A.; Mehta, P.K. Microbial enzymes: industrial progress in 21st century. 3 Biotech 2020, 10, 1–20. (https://doi.org/10.1007/s13205-020-02368-1).
4. Sharma, R.K.; Choudhary, R.; Sharma, K. Role of microbes in industrial wastewater treatment: A review. Environ. Sustain. 2018, 1, 191–204. (https://doi.org/10.1007/s42398-018-0025-z).
5. Strong, P.J.; Claus, H. Laccase: A review of its past and current application in bioremediation. Crit. Rev. Environ. Sci. Technol. 2011, 41, 373–434. (https://doi.org/10.1080/10643380902945706).

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

the details are contained in my written comments attached in the pdf . 

Comments for author File: Comments.pdf

Comments on the Quality of English Language

there is need to rephrase and relook some paragraphs as highlighted in yellow in the original paper and attached comments pdf 

Author Response

Reply to Reviewer 2

Section	Issue of concern	Reviewers comments
Title	Line 3	Contamination of which ecosystems?   Author response: The title has been revised. In particular the ecosystem is added. Please see the revised title.
Abstract         Key words	Line 17           Line 26             Line 31	Functional enzymes on which ecosystem?   Author response: Revised. Please see the revised abstract.   Alter the chemicals structure of heavy metals in water, soil or air?   Author response: We apologize for this inconvenience. The spotted sentence has been revised suitably.   Consider adding bioremediation Legislative Author response: Added: environmental policy
Introduction	Line 48	What is the difference between soils and terrestrial ecosystem?   Author response: The soils meaning arable soils and terrestrial ecosystem covering a holistic ecosystems. This issue is revised accordingly. Please see the revised introduction.   Though –check spelling Is USEPA a global regulatory body?   Author response: USEPA has been deleted. Thanks for this concern.   What are global environment concern?   Author response: The heavy metal contamination pertaining the overall environmental matrix including soils, water, and industries.   What do you mean by soil and environmental samples?   Author response: Replaced by water samples.   of those approaches are still in question   Author response: Revised. The physical and chemical remediation and their sustainability still debatable.   what is OMICS approaches? –   Author response: Revised What is contaminated samples?   Author response: Revised.   What about the role of legislative governance on bioremediation as an objective?   Author response: This review focuses on research trend and limitations of microbial remediation of heavy metal contamination of soils and water samples. Thus, legislative governance should be trimmed as previous review has already address this issue meticulously.   Sarker et al …… is over cited, was it the only author for this review?-     Author response: Revised
	Line 65 Line 66
	Line 71
	Line 80
	Line 89
	Line 99 Line 103
Global Challenge of Heavy Metal Pollution	Line 139         Line 173   Figure 1 (a) and (b)	Are sources of heavy metal contamination exclusively mentioned?   Author response: The authors apologize for this inconvenience. In general, sources of heavy metal is a vast research area. We, hereby, squeezed the theme for brevity of this specific section and keeping more space microbial remediation and their discussion.     Are Hg, Pb, Cd, As, Cr the only heavy metals?   Author response: We apologize for the inconvenience. These are some exemplary heavy metals. Thank you for your consideration.   The contamination of human food Are these figures original work of authors or adopted from other authors?   Author response: The figure is original work of the author. There is no issue of copyright. The information was modified from earlier study and cited in the revised capiton.
Current Global Trend of HM Remediation Strategies	Line 216   Line 229   Line 244	Bioremediation as a technique relies   Author response: Revised.   Is the electrocoagulation process a bioremediation technique?   Author response: We apologize for this inconvenience. The electrocoagulation has been discussed as advanced remediation process along with nanoremediaion.   What do the author mean by traditional remediation method?   Author response: Traditional means physical and orthodox chemical process of heavy metal remediation.

 

	Line 249	Is Fig 2 the original work of the authors?   Author response: The figure 2 is the original work of the author.
Microbial Bioremediation of HM- An Overview	Line 552 Line 259- 261   Fig 3 and 4           Bacterial Bioremediation, Fungal Bioremediation, Algal Bioremediation, Microbial Consortia-Based Bioremediation,	living organisms only ? cite source of information in those lines-   Author response: Revised Are these figures original work of authors or adopted from other authors?   Author response: Yes. The figures are original work of the author.   The authors to relook paragraphs 373- 374 and 397- 399 (Basicallt repeated sentences in 422-425)—   Author response: Revised   The authors cited in these sub heading are very few. Let authors add more authors who have done similar work Explanation in line 429-431 should have been done in the beginning of the current topic -- Author response: Revised
Underlying Mechanisms of Microbial Bioremediation	Line 357	biosorption, biotransformation, bioaccumulation, and bioleaching. These process need further explanation in detail why is co-metabolism missing? Line 466-467 and 478- 479 are repetition   Author response: These issues already been addressed in earlier research (e.g., Sharma et al., 2022), thus, those points has been trimmed to avoid potential redundancy.   How are the microbes engineered?-   Author response: Revised   How is horizontal gene transfer carried out?-   Author response: Revised   Though, a major challenge in utilizing these GEMs in real- world conditions is maintaining the population of recombinant bacteria in soil. Explain further this paragraph metal bioremediation can be a?? effective option to mitigate the potential hazards associated   Author response: Revised
	Line 524- 525
	Line 530-531
	Line 379
Multi-Omics Approach for Enhanced Bioremediation	Line 397-399	The new environmental management techniques and opportunities that the omics, transcriptomics, metagenomics, 398 proteomics, and related fields added to the molecular science took care of (relook this

 

		sentence)-Revised basically repeated (397-399 (Basicallt repeated sentences in 422-425) Omics technology refers to a molecular biological approach that enables simultaneous analysis of biomolecules such as DNA, RNA, proteins, and metabolites from individual organisms as well as the entire community should have come first in line 407 Revised-In the manuscript
Prospects and Limitations	Table 1	Check areas highlighted in yellow
Practical Challenges and Recommendations	the vital limitations and practical challenges concerning bioremediation of HM under different subheadings are work of others	Cite authors for each subheading discussed   Author response: Thank you for your kind suggestion. This section is a novel section of this review. Many new ideal has been incorporated as innovative approach, as a result, the related citations cannot be amended.     Rephrase the sentence in line 536 What does the author mean by in terms of economic perspective   Author response: Thank you for this suggestion. The spotted section has been revised-In the manuscript
Conclusions	biomineralization, biostimulation, mycoremediation, cyanoremediation, phytodegra- 545 dation, phytostabilization, hyperaccumulation, dendroremediation, and rhizofiltration	These processes should have been discussed in details with clear explanation for the readers because this is review work.   Author response: Thank you for your kind suggestion. The detailed explanation of those processes has already been published earlier (e.g., Sharma et al. 2022; Khalid et al. 2018; Sarker et al. 2023). Thus, to avoid potential redundancy, a detailed explanation was not incorporated in this review. On the other hand, this review particularly focusing of the microbial potentiality, current research gap and mechanistic insight.
		Create a new title and discuss biosafety standards as a topic of its own under this review-   Author response: As per suggestion, a new section has been added (2.5. Biosafety Standards in Nano-Bioremediation)   What about bioremediation using animals? Nothing has been mentioned in regard to that. What is the difference between bioremediation and phytoremediation?   Author response: Thank you for your excellent suggestion. This review particularly focusing on the microbial remediation of heavy metals and their research pitfall following the vital recommendations. The bioremediation using animal has not been considered for this current study. The author apologize for this inconvenience. In another note, phytoremediation is a part of bioremediation.
General comment	Comprehensive Review	The work is relevant but the review has not cited several authorities who have done a lot of work in this area. A review paper should cite and review all work in the related field.   Author response: Thank you for your excellent observation. The author agreed with reviewer. The review regarding heavy metals had been published in early years. However, this review pinpointing the key research gap and suggesting recommendations for boosting the bioremediation of heavy metals in soils and water ecosystem. Thank you for your kind consideration.

 

 

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

I suggest that the authors pay attention to all parts highlighted in yellow. 

Let the authors introduce all figures and tables in the manuscript before introducing them

Figures in the manuscript that have been adapted by authors from other work need to be cited appropriately.

Figures created by the authors should also be cited as work of authors, 2025

Comments for author File: Comments.pdf

Comments on the Quality of English Language

Let the authors improve on some words highlighted in yellow

Author Response

Dear Colleague,

Please, find the attached file.

Thank you so  much for your critical thinking and valuable suggestions.

 

Author Response File: Author Response.pdf