the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Mineralization Mechanism and Application Potential of Vaterite Induced by Two Bacterial Strains
Abstract. Clarifying the bacterial mechanisms underlying vaterite biosynthesis is important for advancing biomineralization theory and expanding its applications in material science, environmental protection, and biomedicine. In this study, Bacillus velezensis LB002 and Pseudomonas putida KT2440 were used as representative bacterial strains to compare strain-dependent vaterite formation and environmental remediation performance. The biomineralization processes in the liquid medium were dynamically monitored, and the induced biominerals were characterized, with particular attention to their organic components. The differences in vaterite characteristics between both bacterial systems were evaluated, and their remediation potential was assessed using Cu2+ and tetracycline removal as model applications. Both strains induced vaterite formation under identical culture conditions, while B. velezensis exhibited a stronger biomineralization capacity than P. putida. In a 100 mL culture system, the Ca2+ mineralization percentage of B. velezensis reached 35.06 %, and the dry weights of biomineral aggregates produced by B. velezensis and P. putida were 0.36 and 0.31 g, respectively. SEM observations revealed that the vaterite induced by B. velezensis had a loose and porous surface, whereas that induced by P. putida had a relatively smooth surface. For the high concentration of Cu2+ at 50 mg/L, the removal rate reached 84.93 % for B. velezensis-induced vaterite, compared with 71.86 % for P. putida-induced vaterite under the same conditions. Both biominerals demonstrated similar tetracycline removal performance, with removal rates of approximately 60 %. These findings provide comparative evidence for strain-dependent vaterite formation and support the potential application of biogenic vaterite in environmental remediation.
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Status: open (until 29 Jul 2026)
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RC1: 'Comment on egusphere-2026-3126', Anonymous Referee #1, 16 Jun 2026
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AC1: 'Reply on RC1', Xiaofang Li, 24 Jun 2026
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This manuscript compares vaterite formation in Bacillus velezensis LB002 and Pseudomonas putida KT2440 and tests the resulting biominerals for Cu²⁺ and tetracycline removal. The experimental design is coherent and the subject is worth attention. That said, the mechanistic claims are pushed well beyond what the data can support, and the environmental application section reads more like an ad than a «Results» discussion.
We sincerely appreciate your pertinent and constructive comments. We have extensively revised the Discussion section and modified several overstated descriptions in the Abstract and Introduction. The detailed revisions addressing your concerns are presented as follows:
Regarding overextended mechanistic inferences unsupported by experimental data.
Subsections 4.1 and 4.2 of the Discussion have been fully rewritten. All mechanistic analyses are strictly confined to interpretations validated by the measured parameters of this study, including carbonic anhydrase activity, extracellular polysaccharide/protein contents, organic matter proportion via thermogravimetric analysis, micro-morphology observed under scanning electron microscopy, BET specific surface area, XRD crystalline phases, carbonate content determined by acid-base titration, and biomineralization experimental results. All speculative microscopic molecular regulatory mechanisms lacking direct experimental evidence have been removed or toned down, such as the elaborate process of crystal nucleation mediated by cell wall templates and the complete intracellular biomineralization metabolic pathway. All statements linking strain properties, extracellular metabolites to vaterite morphology and mineralization efficiency are directly supported by quantitative data obtained in this work. All revised passages in the manuscript are highlighted in red.
Regarding promotional and overstated descriptions in the environmental application section
We have comprehensively revised Subsection 4.3 (Environmental application potential) and abandoned promotional wording, replacing it with objective analyses grounded in experimental data. All overblown statements regarding engineering application prospects have been eliminated. Analyses of remediation performance are restricted solely to batch adsorption results obtained under laboratory conditions in this study, with a clear distinction drawn between laboratory simulation data and on-site remediation efficacy. We objectively elaborate the practical limitations identified in this work, including the high cost of LB medium, long mineralization cycle, and low mineral yield per unit volume. Additionally, we rationally discuss the limited pollution treatment scenarios suitable for biogenic vaterite.
- All overstated promotional language was removed and experimental boundaries were clearly defined.
Qualifying phrases including under the laboratory test conditions, within lab-scale static batch systems, laboratory-prepared co-contaminated solution and lab-scale adsorption data were newly added to strictly distinguish simulated experimental systems from actual field environments. Expressions such as "expand application potential" were deleted entirely.
- The term "remediation" was downplayed and the applicable scope narrowed down. Phrases repeatedly appearing in the original manuscript including large-scale pollution remediation and remediation efficiency were all replaced with neutral alternatives: treatment and pollutant immobilization performance. The conclusion explicitly states that the material is only suitable for pretreatment at small-scale, heavily polluted sites, and rules out its feasibility for full-scale in-situ remediation across broad areas.
Minor Revisions
In line with the revisions made to the Discussion section, we have fine-tuned overly optimistic and exaggerated statements regarding the material application potential in the Abstract and Introduction. Only objective conclusions backed by comparative experimental data are retained. The Conclusion section has also been streamlined accordingly to guarantee that all viewpoints throughout the manuscript are fully evidence-based.
All the above revisions are marked in the manuscript.
Major comments
- The mechanistic arguments are overstated, in places considerably so. Cell wall properties, carbonic anhydrase activity, extracellular proteins and polysaccharides are all proposed as regulators of vaterite formation and morphology, but the evidence for each remains correlative. The EPS and protein-mediated nucleation claims, in particular, have not been demonstrated, only suggested. The authors should scale these back and be explicit, throughout, about the boundary between what was measured and what is being inferred. This distinction matters and, in my opinion, the manuscript blurs it.
We appreciate your suggestions. We have thoroughly revised Subsection 4.1 of the Discussion, and all relevant revisions are marked in the manuscript. All absolute statements in the text have been adjusted, with detailed modifications summarized below. Furthermore, the biomineralization experiments confirm that extracellular proteins facilitate vaterite formation (Fig. S2), which provides supporting evidence that proteins exert certain effects during vaterite induction. Corresponding descriptions addressing this point have also been reworded in the manuscript.
1.Original sentence: The cell wall properties and EPS composition can affect both the crystal type and micromorphology of biogenic calcium carbonate.
Revised to: Cell wall characteristics and EPS profiles show correlations with the crystal phase and micromorphology of biogenic calcium carbonate.
2.Original sentence: Among EPS components, proteins are particularly important because they provide nucleation sites for vaterite formation (Zhang et al., 2021; Gao et al., 2023).
Revised to: Existing studies proposed that proteins may serve as potential nucleation sites for vaterite crystallization (Zhang et al., 2021; Gao et al., 2023), which is consistent with the correlative trends observed in our work.
3.Original sentence: These observations suggest that the morphology of biogenic vaterite is largely regulated by the composition, type, and abundance of EPS in the fermentation broth.
Revised to: These morphological differences imply a potential link between vaterite microstructure and the composition, category and relative abundance of EPS in the culture system.
4.Original sentence: Vaterite synthesis induced by the two bacterial strains was governed by the combined effects of bacterial cell wall properties, extracellular metabolites, and mineralization conditions
Revised to: Variations in vaterite biosynthesis between strains are correlated with cell wall features, extracellular metabolites and culture conditions.
5.Original sentence: Extracellular metabolites, particularly proteins and polysaccharides, are key regulators of extracellular bacterial mineralization.
Revised to: Extracellular metabolites (especially proteins and polysaccharides) exhibit strong correlations with extracellular biomineralization behavior.
6.Original sentence: The higher Ca2+ mineralization rate and larger specific surface area of B. velezensis-induced vaterite indicate that this biomineral has greater potential for practical application.
Revised to: The higher Ca²⁺ mineralization efficiency and larger specific surface area of vaterite from B. velezensis provide comparative basic laboratory data for subsequent research on pollutant removal materials.
All the above relevant revisions have been marked in the manuscript.
- The Gram-positive/Gram-negative framing is an oversimplification that ends up obscuring more than it reveals.B. velezensisand P. putida differ in cell morphology, metabolism, and secreted biomolecules well beyond their cell wall structure. Treating Gram status as the primary explanatory variable when so many other things differ between these two organisms is not a defensible interpretive choice. The framing should be rethought: these are two distinct biological systems that produce different mineralization phenotypes, and the discussion should say so plainly.
Thank you for your comments. Corresponding to Subsection 4.2 of the Discussion, we have revised this section as follows:
In addition, the two strains exhibit distinct cell wall architectures: Bacillus velezensis possesses a thick peptidoglycan layer typical of Gram-positive bacteria, whereas Pseudomonas putida has the thin cell wall structure characteristic of Gram-negative species. Previous studies speculated that peptidoglycan, as well as carboxyl and phosphate functional groups on teichoic acids, may interact with free Ca²⁺ and serve as potential mineralization templates (Zhang et al., 2021; Li et al., 2023a). Nevertheless, cell wall structural divergence constitutes merely one of many physiological and structural disparities between these two phylogenetically distant strains. In fact, the divergent mineralization phenotypes detected in our system correlate with the combined effects of strain-specific carbonic anhydrase activity, EPS secretion patterns and inherent metabolic differences.
- The statistical reporting is insufficient and needs to be addressed properly. Three biological replicates are mentioned, but there is no discussion of statistical power, variance structure, or how multiple comparisons were handled. I think this matters, especially for the time-series and adsorption data, for which the risk of false positives is real. No processing code or data repository is referenced anywhere (the Suppl. Mat. data is not sufficient in this case). The authors should specify which tests were applied, where, and how the data were processed from raw output to reported values.
Response to Reviewers' Comments: We sincerely appreciate the reviewer’s valuable and rigorous suggestions on standardized statistical reporting and data transparency, and comprehensive revisions have been supplemented in the revised manuscript accordingly:
A dedicated subsection 2.6 Statistical analysis has been newly added in the Materials and Methods. We clearly stated that all experiments were conducted with three independent biological replicates. Before formal significance testing, Shapiro–Wilk test and Levene’s test were applied to evaluate data normality and variance structure. One-way ANOVA combined with Tukey’s HSD multiple comparison test was adopted for time-series and adsorption datasets; Tukey adjustment effectively controls the family-wise error rate and reduces the risk of false positives caused by multiple pairwise comparisons. All statistical calculations were implemented via IBM SPSS Statistics 20. Given the fixed three biological replicates experimental design in this study, formal statistical power calculation was not performed, which we have acknowledged implicitly by adopting strict multiple comparison correction to lower false positive probability.
A Data Availability section has been supplemented at the end of the manuscript. All raw instrumental measurement datasets supporting our results are fully deposited in Supplementary Materials, which contain complete records of raw data. No self-compiled processing scripts were used in this work; statistical computation relied on SPSS, while data collation and graph plotting were finished using the built-in functions of Excel and Origin.
Since we did not upload datasets to a public data repository, we clarify that further complete original experimental records can be obtained from the corresponding author upon reasonable research requests to improve data accessibility and repeatability. Full manual data preprocessing steps (background subtraction, outlier screening, averaging of replicate groups) are also documented within Supplementary Materials to illustrate the whole workflow from raw instrument outputs to the averaged values presented in figures.
The following contents have been supplemented in the section of Material and Methods in the revised the manuscript:
2.6 Statistical analysis
All experiments in this study were performed with three independent biological replicates. Prior to statistical testing, Shapiro–Wilk test and Levene’s test were separately conducted to assess the normality and homogeneity of variance (variance structure) of all datasets. One-way analysis of variance (ANOVA) was used to test whether the overall differences between groups were statistically significant, followed by Tukey’s HSD multiple comparison test to further determine which specific groups had significant differences. All statistical analyses were completed using IBM SPSS Statistics 20.
Data availability.
All raw experimental datasets supporting the findings of this study are included within Supplementary Materials. All statistical analyses and figure plotting relied on built-in functions of Excel and Origin. Supplementary files contain full records of all raw data. They correspond to the files Raw data for Figure 1, 2, 3 and 6, respectively.
- The application claims go beyond what the results support. Controlled batch adsorption is a useful starting point. It is not evidence of remediation potential, and the manuscript should not implying otherwise. The single-point batch design, no regeneration or reuse testing, clean matrices instead of soil pore water or real wastewater, all of these are not minor caveats to mention; they are genuine constraints on what can be concluded. They deserve explicit treatment.
Thank you for your suggestions. We have revised Subsection 4.2 (Mineral Adsorption Performance) and Section 5 (Conclusions). The detailed revisions are presented as follows:
1)The following definitive statements have been removed:
such as practical soil remediation、great prospect for wastewater treatment、excellent field remediation potential、can be applied to actual polluted water/soil
2)All statements have been toned down into qualified descriptions:
The vaterite synthesized in this study exhibits adsorption performance under single-point static batch systems, which can provide basic data and reference for subsequent remediation-related research.
3)An independent statement of research limitations has been added at the end of Subsection 4.2.
Notably, the present adsorption results were obtained only from single-point static batch tests in artificial clean solution without regeneration assays, which cannot fully represent the material’s performance in complex real wastewater or soil pore water, and thus cannot be directly extrapolated to practical field remediation scenarios.
Conclusion section
Sentences regarding engineering applications, soil remediation and practical wastewater treatment at the end have been deleted and revised as follows:
The adsorption data obtained in this research provide fundamental data and references for the further research on the treatment for the pollution combined by heavy metal ions (such as copper ions) and antibiotics (such as tetracycline).
- The organic matter interpretation needs more restraint. Higher N, C, H, and TG-DTG values in theP. putidaproduct may well reflect residual cells and non-mineralized biomass rather than matrix-incorporated organics: the Methods section actually acknowledges this, which makes it more puzzling. Indeed, the Discussion then uses these same bulk measurements to support mechanistic conclusions they are not precise enough to carry. The authors should go back to this section and reconsider what these data actually show.
We appreciate the critical comments raised by the reviewer regarding the overinterpretation of TG-DTG and elemental organic matter data. We fully agree with this viewpoint: relying solely on bulk elemental contents and thermogravimetric signals cannot distinguish organic components tightly incorporated inside vaterite crystals from intact residual bacterial cells and unmineralized biomass attached to the surface of mineral aggregates. To address this concern, we have extensively revised Section 4.2 and restrained overreaching mechanistic speculations, with detailed revisions listed below:
The elevated C, N, H contents and thermogravimetric weight loss values of products derived from Pseudomonas putida may originate from residual bacterial cells, biomass within the system, as well as organic moieties embedded in the vaterite crystal lattice.
All statements establishing definitive causal links between total organic matter content and crystalline phase regulation have been removed and uniformly rephrased using correlative descriptions. We also emphasize that the available bulk measurements only reflect the total organic load of aggregates and fail to differentiate intracellular residual substances from organic fractions at mineral interfaces.
All revisions are marked with revision tracks in the revised manuscript. We have reorganized the logical flow of discussions related to organic matter to ensure all conclusions are strictly confined to interpretations supported by the available analytical data.
Original text: The weaker mineralization performance of P. putida was supported by organic matter and carbonate analyses. TG-DTG results showed that P. putida-induced biogenic vaterite contained a higher organic matter content, indicating that its bacteria–mineral aggregates retained more unmineralized bacterial cells or organic components. This higher organic fraction corresponded to a lower mineralization-inducing capacity in the P. putida system. Quantitative carbonate titration showed that the carbonate content of P. putida-induced vaterite was approximately 14.7% lower than that of B. velezensis-induced vaterite, confirming that organic components accounted for a larger proportion of the former mineral structure (Figs. 2a and S1b).
Revised to:
Thermogravimetry-derivative thermogravimetry (TG-DTG) results reveal that precipitates produced by Pseudomonas putida exhibit stronger total organic signals. Such organic matter likely originates from three major sources: residual intact bacterial cells or unmineralized organic substances attached to the surface of mineral aggregates, as well as partial organic components embedded within the vaterite crystal framework. Macroscopic thermal analysis and elemental detection alone cannot distinguish lattice-incorporated organic matter from bacterial debris adhering to mineral surfaces. Quantitative carbonate titration indicates that the carbonate content of vaterite biomineralized by Pseudomonas putida is approximately 14.7% lower than that of products generated by Bacillus velezensis (Fig. 2a, Fig. S1b). This observation demonstrates a larger proportion of biological residues within the mineral aggregates of the former strain. Combined with the calculated calcium mineralization efficiencies (35.06% for B. velezensis and 27.50% for P. putida), these data prove that Bacillus velezensis possesses a higher calcium mineralization rate and thus superior biomineralization capacity.
Minor comments
6."Potential application" in the abstract needs hedging as the data are preliminary and the current wording overpromises. Some of the comparative claims about biogenic vaterite in the introduction belong in the literature background, not in the study rationale.
Thank you for your suggestions. We have revised the opening and closing sentences of the Abstract and adjusted the limitations on application prospects. We also reorganized the paragraphs in the Introduction. In the original manuscript, literature discussions on the adsorption performance of Bacillus velezensis-derived biogenic vaterite and its comparison with conventional adsorbents were mixed with the research rationale, blurring the boundary between literature background and research motivation.
In this revision, the Introduction has been restructured into separate paragraphs:
All previously reported findings regarding the adsorption performance of biogenic vaterite and comparisons of material advantages and disadvantages are consolidated into a dedicated literature review paragraph to systematically summarize current research progress and existing deficiencies. Subsequent independent paragraphs exclusively address the status of combined copper-tetracycline pollution in farmland, identified research gaps, the rationale for strain screening, and experimental design, without interspersing comparative literature descriptions.
All the above revisions are highlighted in red in the manuscript.
- A schematic showing the proposed connections between pH, carbonic anhydrase activity, EPS composition, morphology, and adsorption would genuinely help. I think that the mechanistic argument is hard to follow as prose alone, and this is one case where a figure would earn its place.
We have substantially revised Figure 7 into a mechanistic schematic to intuitively illustrate the full correlations among pH, carbonic anhydrase activity, EPS composition, mineral morphology and adsorption capacity. Annotated directional arrows were added to show the stepwise regulatory pathway, and explanatory text was supplemented beside the two types of vaterite to compare their adsorption performance.
Fig. 7 Proposed schematic model of calcium carbonate mineralization and combined pollutant immobilization induced by the two bacterial strains.
- Please confirm that the abiotic LB/CaCl₂ control stayed precipitation-free across the full incubation; this is a basic check and it is not clearly reported.
Thank you for pointing out the insufficient description of the abiotic control.
We clearly confirm that the abiotic LB/CaCl₂ system remained clear without any precipitate throughout the incubation. We have supplemented this result in the revised text (Lines 141–144): No visible precipitate was found in the abiotic control group at all sampling time points during the entire 14-day incubation, ruling out spontaneous mineral precipitation caused by simple chemical mixing of LB medium and CaCl₂.
- The tetracycline discussion should also acknowledge that the removal mechanism almost certainly differs from Cu²⁺ binding: pH, surface charge, and competitive complexation all matter here and none of them is discussed.
We supplemented targeted discussions on the differential adsorption mechanisms of tetracycline and Cu²⁺ in Section 4.2. We briefly analyzed how pH, mineral surface charge and competitive complexation regulate tetracycline removal efficiency, and clarified that these three factors can significantly alter tetracycline adsorption performance under varied environmental conditions. Meanwhile, we have stated that all experiments in the present study were conducted under limited experimental conditions, and multi-gradient tests are required in further research to quantitatively characterize the above influencing rules. The detailed contents are as follows:
Unlike Cu²⁺ immobilization dominated by surface coprecipitation and complexation, tetracycline adsorption is co-regulated by system pH, mineral surface charge and competitive complexation effects. pH modulates the surface charge properties of vaterite aggregates and the dissociation speciation of tetracycline molecules, thereby altering electrostatic attraction between them. In addition, coexisting ions and organic ligands in environmental media may occupy adsorption sites and generate competitive complexation effects that hinder tetracycline immobilization. The batch experiments carried out in this work only reveal the basic removal capacity of biogenic vaterite for tetracycline in the limited experimental conditions. Further pH gradient tests and control groups with coexisting solutes are necessary to quantitatively elucidate the regulatory patterns of the three key factors on tetracycline retention performance.
Recommendation
Major revision. The study addresses an interesting question, and the core results are publishable but not in the current form. The mechanistic overreach, the statistical gaps, and the application overclaiming, each need substantive attention and not simple cosmetic revision. The authors have something worth publishing; the manuscript just needs to be more convincing about what it shows.
We sincerely appreciate the reviewer’s overall evaluation and constructive comments on our manuscript. Following the suggestions, we have implemented substantial in-depth revisions instead of merely superficial linguistic polishing: all conclusions are strictly constrained within the scope supported by our experimental data, complete standardized statistical descriptions are supplemented, laboratory simulation results are objectively distinguished from practical field scenarios, and we refrain from overextrapolating the material’s field remediation potential. All revisions to the main text and figures are marked with track changes for easy inspection. We believe these extensive modifications have greatly strengthened the argumentation and scientific rigor of this work, and we respectfully invite you to review the full revised manuscript.
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AC1: 'Reply on RC1', Xiaofang Li, 24 Jun 2026
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This manuscript compares vaterite formation in Bacillus velezensis LB002 and Pseudomonas putida KT2440 and tests the resulting biominerals for Cu²⁺ and tetracycline removal. The experimental design is coherent and the subject is worth attention. That said, the mechanistic claims are pushed well beyond what the data can support, and the environmental application section reads more like an ad than a « Results » discussion.
Major comments
Minor comments
"Potential application" in the abstract needs hedging as the data are preliminary and the current wording overpromises. Some of the comparative claims about biogenic vaterite in the introduction belong in the literature background, not in the study rationale. A schematic showing the proposed connections between pH, carbonic anhydrase activity, EPS composition, morphology, and adsorption would genuinely help. I think that the mechanistic argument is hard to follow as prose alone, and this is one case where a figure would earn its place. Please confirm that the abiotic LB/CaCl₂ control stayed precipitation-free across the full incubation; this is a basic check and it is not clearly reported. The tetracycline discussion should also acknowledge that the removal mechanism almost certainly differs from Cu²⁺ binding: pH, surface charge, and competitive complexation all matter here and none of them is discussed.
Recommendation
Major revision. The study addresses an interesting question, and the core results are publishable but not in the current form. The mechanistic overreach, the statistical gaps, and the application overclaiming, each need substantive attention and not simple cosmetic revision. The authors have something worth publishing; the manuscript just needs to be more convincing about what it shows.