Review Reports - A Bibliometric Analysis of Global Research Hotspots and Progress on Microbial Extracellular Polymeric Substances in Bioremediation

Round 1

Reviewer 1 Report (New Reviewer)

Comments and Suggestions for Authors

This manuscript presents a bibliometric analysis of research on extracellular polymeric substances (EPS) in bioremediation, covering 2005–2025, using VOSviewer and CiteSpace. The authors identify a thematic shift from structural characterization toward interactions with emerging pollutants (microplastics, antibiotics, ARGs). They also review mechanistic roles of EPS in adsorption, electron transfer, and degradation. The topic is timely and relevant to the journal’s scope. However, the paper suffers from several major issues: the bibliometric methods lack transparency and reproducibility, the integration between quantitative analysis and mechanistic review is weak, and many claims are not directly supported by the presented data. A major revision is required.

Lines 123–135: The search strategy is described, but crucial details are missing. The query TI = ("extracellular polymeric substance*" OR "EPS") AND TS = ("microb*" OR "bacteria" ...) is too broad and likely includes many irrelevant papers (e.g., EPS in food science or medical biofilms). No validation of the 597 final papers is provided (e.g., manual screening or inter-rater agreement). Without this, the dataset’s relevance is uncertain. Provide a PRISMA-style flow diagram and report how many papers were excluded at each step, with reasons.
The search period is set to Jan 2005 – Dec 2025 (line 131). Including a future date (Dec 2025) is nonsensical. If this is a typo, correct to Dec 2024 or the actual search cutoff. If not, this is a critical error.
Lines 322–324 state that “interaction mechanisms between EPS and emerging pollutants represent a primary research hotspot.” However, the keyword co-occurrence (Fig. 6a) and timeline (Fig. 6b) do not provide quantitative evidence that “microplastics” or “ARGs” are dominant hotspots. The figures show many clusters, and the average publication year sequence (Fig. 6b) is too low-resolution to read. The claim is therefore overreaching without citation burst or frequency trend analysis. Add a table of top-20 keywords with year of emergence and burst strength, or remove overgeneralized statements.
The paper tries to be both a bibliometric analysis and a mechanistic review. This leads to redundancy and weak integration. For example, Section 4 (current research progress) repeats mechanisms already cited in Table 3 and Fig. 7, but the bibliometric data are not used to justify whythese mechanisms are selected as “hotspots. Either reframe as a bibliometric study with a brief discussion of top-cited mechanisms, or as a focused review. If hybrid, explicitly link each mechanistic subsection to a keyword cluster or burst.
Lines 80–86 describe S-EPS, LB-EPS, TB-EPS with corrosion examples, but later in Section 5.2.3 the authors call for “functional resolution of EPS fractions” as a future direction. This is internally inconsistent. Moreover, in Table 3 and Section 4.1, most studies do not distinguish which EPS fraction is responsible. This is a major knowledge gap that should be acknowledged earlier and more critically. Add a clear statement in Section 4 that most current studies use total EPS, and therefore, the mechanistic claims may oversimplify real systems.
Lines 650–670 (Challenges) correctly note low yield and high cost, but the abstract and conclusion still imply near-term applicability. The phrase “waste valorization” (Section 5.2.1) is vague – no concrete yield data or cost comparison with existing technologies is provided. Without techno-economic estimates, this remains aspirational.
Line 42–43:“rather than transferring pollutants between forms or media” – This sentence is incomplete. Rewrite for clarity.
Line 78:“S- EPS, LB- EPS, TB- EPS of were successfully extracted” – Typo: remove “of”.
Line 123:“The flowchart of this study is shown in Fig. 1” – Figure 1 is missing from the provided PDF. Please ensure all figures are included.
Figure 4a: The bar chart for China (390 publications) vs. the USA (70) is dramatically different, but no statistical test is applied. Add a note that raw counts are influenced by database coverage and research funding.
Figure 5 (author network): The resolution is poor; node labels are illegible. Provide a higher-resolution image or a table of top collaboration clusters.
Line 366: “Filipa Rodrigues et al.” – First names should not be used. Change to “Rodrigues et al.”
Line 401: “1,000 mg/L EPS from Brucella intermedia” – This concentration is extremely high and environmentally irrelevant. Add a caveat that such doses are not feasible in real remediation.
Line 542–545:The discussion on EPS facilitating ARG transfer via HGT is important but speculative. Provide a more balanced view – current evidence is mostly from lab strains (e.g., coli or Geobacter), not real environmental consortia.

Comments on the Quality of English Language

The English could be improved to more clearly express the research.

Author Response

We would like to express our sincere gratitude to the reviewer for the constructive and professional comments on our manuscript (microorganisms-4275243). These comments have been carefully considered, and we have revised the manuscript accordingly. We provide point-by-point responses and the revised content.

Please see the attachment for details.

Author Response File: Author Response.pdf

Reviewer 2 Report (New Reviewer)

Comments and Suggestions for Authors

i checked all the revised sentences and it seems ok therefore i have no further questions

Author Response

Reviewer 3 Report (New Reviewer)

Comments and Suggestions for Authors

The manuscript addresses a relevant topic, namely the role of extracellular polymeric substances (EPS) in bioremediation, using a bibliometric approach. The overall structure is clear, and the use of Web of Science together with VOSviewer and CiteSpace is methodologically appropriate. However, in its current form, the manuscript remains largely descriptive and does not yet provide sufficient analytical depth to constitute a strong contribution to the field.

Major comments:

1) A key limitation is that the results are presented mainly as standard bibliometric outputs without deeper scientific interpretation. For example, the increase in publication numbers over time and the dominance of countries such as China and the United States (as shown in the results section) reflect well-established global publication trends rather than insights specific to EPS-related bioremediation research. These observations are expected and do not, by themselves, advance understanding of the field.

2) The keyword co-occurrence and clustering analysis also require more substantive interpretation. While clusters related to “biofilm”, “heavy metals”, “adsorption”, and “wastewater treatment” are identified, the manuscript does not sufficiently explain how these clusters reflect distinct mechanistic roles of EPS in bioremediation processes. For instance, EPS are known to influence contaminant immobilization, microbial protection, and mass transfer processes, yet these aspects are not clearly connected to the identified keyword clusters. As a result, the analysis remains at the level of classification rather than interpretation.

3) In addition, although a substantial dataset was analyzed (782 initial records reduced to 597 after filtering, as shown in Figure 1), the manuscript does not provide a critical synthesis of the underlying literature. Highly cited papers are identified, but their scientific contributions are not discussed in detail. A stronger manuscript would analyze why certain works are highly cited and how they have shaped current research directions.

4) The methodological section would also benefit from further clarification. The search strategy relies exclusively on the Web of Science Core Collection, and although keywords such as “extracellular polymeric substance*” and “EPS” are used, it is not clear how sensitive and specific this query is. For example, the term “EPS” is ambiguous and may retrieve irrelevant records. The authors should discuss potential biases associated with the search strategy and database selection.

5) Another important limitation is the lack of integration between bibliometric findings and practical or experimental implications. The manuscript identifies “hotspots” and emerging trends, but does not clearly translate these into concrete research needs or directions. For example, it remains unclear how the identified trends could guide future studies on EPS-mediated contaminant removal or bioremediation system design.

To improve the manuscript, the following revisions are recommended:

- Provide a deeper interpretation of keyword clusters by explicitly linking them to known mechanisms of EPS involvement in bioremediation.

- Expand the discussion of highly cited papers to explain their scientific impact rather than simply listing them.

- Critically evaluate the search strategy and discuss its limitations, including potential ambiguity of keywords and database coverage.

- Move beyond descriptive results and clearly articulate the novel insights generated by this bibliometric analysis.

- Strengthen the conclusions by identifying specific, scientifically grounded directions for future research.

In its current form, the manuscript is methodologically sound but largely descriptive. Substantial revision is required to enhance its analytical depth and scientific contribution.

Author Response

Please see the attachment for details.

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report (New Reviewer)

Comments and Suggestions for Authors

The revised manuscript has improved substantially compared with the previous version. The authors have addressed several important concerns raised during the first review round, particularly by strengthening the interpretation of the bibliometric findings and expanding the discussion of mechanistic aspects of EPS-mediated bioremediation.

The newly added discussion in Sections 3.1 and 3.3 provides a clearer connection between publication trends and the actual development of EPS-related remediation research, rather than only describing general publication statistics. In addition, the revised keyword clustering analysis in Section 3.5.1 is much stronger than in the previous version, as the identified clusters are now linked to specific functional roles of EPS, including microbial protection, contaminant immobilization, adsorption, and electron transfer processes.

The manuscript has also improved through the expanded discussion of highly cited studies in Section 3.4, where the authors now explain why several foundational papers became highly influential and how they shaped subsequent research directions in the field. The revised “Challenges and Future Perspectives” section is also more focused and better connected to the bibliometric results.

Nevertheless, several issues still require further improvement before the manuscript is suitable for publication.

1) Although the mechanistic discussion has been expanded considerably, some sections still remain descriptive rather than critically analytical. In particular, Sections 4.1.1 and 4.1.2 frequently summarize published findings sequentially (“study X showed…”, “study Y demonstrated…”) without sufficiently discussing inconsistencies, limitations, or unresolved questions across studies. The review would benefit from a more critical synthesis of conflicting results and methodological limitations.

2) The manuscript still combines two different review styles - bibliometric analysis and narrative mechanistic review, but the integration between these components is not always fully balanced. The bibliometric component remains relatively basic and relies mainly on standard co-occurrence and clustering outputs. More advanced bibliometric analyses (for example, co-citation evolution, thematic evolution, or reference burst analysis) would strengthen the scientometric contribution of the work.

3) Some conclusions are stated too strongly considering the nature of the evidence presented. For example, statements such as “This result directly confirms…” (lines 431-433) should be moderated, because bibliometric keyword trends alone cannot directly confirm mechanistic scientific relationships.

4) The discussion regarding EPS fractions (S-EPS, LB-EPS, and TB-EPS) is one of the strongest additions in the revised manuscript. However, this concept appears mainly in the later sections of the paper. Since the authors emphasize fraction-specific functionality as a major future research direction, it would improve the overall coherence of the review to integrate this concept earlier and more consistently throughout Sections 4.1–4.2.

5) The methodological limitations are now acknowledged, which is appreciated. However, the manuscript still relies exclusively on the Web of Science database and a relatively broad search strategy involving the term “EPS”. Additional clarification regarding search specificity and potential exclusion of unrelated records would further improve transparency and reproducibility.

Comments on the Quality of English Language

The English language has improved compared with the previous version, but further editing is still recommended. Some parts of the manuscript contain repetitive sentence structures and overly uniform transitions, particularly in Sections 4 and 5. Careful language polishing would improve readability and scientific style.

Author Response

Thank you for your valuable comments. Detailed responses are presented in the cover letter.

Author Response File: Author Response.pdf

Round 3

Reviewer 3 Report (New Reviewer)

Comments and Suggestions for Authors

Before final acceptance, the authors may still consider a minor refinement of several overly detailed literature-summary passages in Sections 4.1.1 and 4.1.2 in order to further improve readability and maintain focus on broader mechanistic synthesis. However, these remaining issues are relatively minor and do not substantially affect the overall quality and scientific value of the manuscript.

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This literature review, titled "A Bibliometric Analysis of Global Research Hotspots and Progress on Microbial Extracellular Polymeric Substances in Bioremediation," offers a comprehensive overview of an important topic. The work is notably well-written and provides an up-to-date overview of the topic.

However, like many contemporary reviews, it falls short of providing critical insights or actionable recommendations that could guide future advancements in the field. Instead, it comes across as another generic overview, lacking the novelty and depth that could truly engage the scientific community.

Given these considerations, I believe this review does not quite reach the level of distinction needed for publication in a journal like Microorganisms.

1. What is the main question addressed by the research?
Reply: None. The Review does not point out any problem or further perspective of a solution or critical points for the area.
2. What parts do you consider original or relevant to the field? What
specific gap in the field does the paper address?
Reply: None. It is a Review that brings nothing new to the area.
3. What does it add to the subject area compared with other published material?
Reply: It's just another generic review written and published without any critical direction.
4. What specific improvements should the authors consider regarding the methodology?
Reply: It's a review without a methodology. But it would have to be rewritten and formulated with points that raise a critical issue and provide direction for the field, and not just a bibliographic survey.
5. Are the conclusions consistent with the evidence and arguments presented?
Reply: No.
6. Are the references appropriate?
Reply: Yes.
7. Any additional comments on the tables and figures and the quality of the data.
Reply: No.

My final decision is to Reject the paper.

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript provides a comprehensive overview of the role of extracellular polymeric substances (EPS) in bioremediation and presents a bibliometric analysis using VOSviewer and CiteSpace. The analysis effectively demonstrates a thematic shift from early studies focused on EPS structural characterization and adsorption mechanisms toward current research emphasizing emerging pollutants, including microplastics, antibiotics, and antibiotic resistance genes (ARGs). The authors highlight multiple mechanisms by which EPS influence pollutant fate, such as adsorption, complexation, degradation, electron transfer, aggregation, biodegradation, gene transfer, and metal reduction.

Overall, the manuscript is well written and addresses a timely and important topic. However, several issues require clarification, correction, and strengthening before publication.

Line 75 refers to Desulfovibrio vulgaris, whereas Reference 17 corresponds to Pseudomonas. This citation mismatch should be corrected.

Similarly, Reference 25 is cited in relation to CiteSpace, but the listed reference pertains to a bibliometric review on biochar in electrochemical energy storage devices. Several citations associated with VOSviewer and CiteSpace also appear to be incorrect. All references should be carefully cross-verified to ensure accuracy and consistency.

Lines 78-80 discuss EPS produced by sulfate-reducing bacteria (SRB). Please clarify whether these EPS are predominantly proteinaceous or polysaccharide-based. Additionally, the differences between soluble EPS (S-EPS) and tightly bound EPS (TB-EPS) in SRB should be clearly explained.

The manuscript would also benefit from a discussion comparing EPS produced under aerobic versus anaerobic conditions, supported by representative examples.

The quality of Figures 2 and 5 is inadequate for publication and should be substantially improved (resolution, clarity, and readability).

In Table 2, row separation and overall formatting need correction to improve readability.

The language used in Lines 195-214 is overly strong and may be perceived as aggressive, particularly in reference to China. This section should be revised to adopt a more neutral and diplomatic scientific tone.

The section on keyword analysis (Section 3.5) would be strengthened by explicitly presenting the underlying data. For example, the authors could include a table summarizing studies on EPS produced by microorganisms, reporting growth temperature and pH, carbon sources, EPS yield (g/L), productivity (g/L/day), molecular weight, key physicochemical properties, biological activities, and relevant references.

The manuscript does not sufficiently discuss the specific roles of EPS in the context of microplastics, nanoplastics, and antibiotic resistance genes, particularly within Section 4 (“Current research progress and hotspots”). The authors should clearly define which ARGs are being discussed and integrate these topics more coherently into the narrative.

Line 527: “EET” should be spelled out at its first occurrence.

Line 538-539: Please clarify whether EPS enhances or inhibits denitrification performance, as the current statement is ambiguous.

Line 552-553: The reduction of As(V) typically increases arsenic mobility. This statement should be corrected accordingly.

Line 569: Please include representative values or examples of EPS productivity reported in the literature.

Line 603: The term “dispersing capabilities” requires further explanation and mechanistic detail.

Additionally, please define “electroactive bacteria” when first introduced.

In summary, while the manuscript addresses an important topic and has strong potential, it requires careful revision to correct citation errors, improve clarity and tone, enhance data presentation, and deepen the discussion of EPS roles in emerging pollutant remediation.