Sand Prawns Mitigate the Impact of Prolonged Drought on the Biology of a Temporary Open/Closed Estuary

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The idea of the paper is interesting. In contrast to generally analyzed environmental factors driving estuarine ecosystem such as studies freshwater inflow, sediment characteristics, and mouth status, the authors tried to analyze the role of the key ecosystem engineer, the sand prawn, Callichirus kraussi. However, I am not convinced by a presentation of results and invite authors to resubmit the Ms after collecting a more sound dataset.

My main concern is linked to a quality of material: only tree repeated experiments for each setting coupled with a little studied volume. This finally resulted in a number of different results under each setting called "outliers".

In addition, preparation of the Ms is inaccurate: many references are missing, section numbering is not consistent, language is  not variable ("conducted" used 11 times) and sometimes unclear ("increases in the biology"). Other comments are below.

Abstract: needs significant linguistic revision: "increases in the biology", etc.
Intro: Li 28-29, "Ecosystem engineers are organisms that change the state of matter, both biotic and abiotic, by alter-28 ing their environments through bioturbation" Not only through bioturbation!
Li 96: please clarify what"macronutrients" are
Salinity and temperature annual variations within the Kasouga Estuary are needed here. I wonder why "Kasouga Estuary supports low levels of phytoplankton and zooplankton biomass" but "benthic communities in TOCEs typically include diverse macrofaunal and meiofaunal assemblages" and "microphytobenthic communities, such as benthic diatoms, also play a significant role in primary production nutrient cycling" That is the trophic basis for that?

Materials and Methods: Li 115 "conducted ranged from 5 to 36 and m-2" ind per sq m?
122 what is "standard length"?

Results: Li 167-169 move to Methods

Four section 5.1.1 - 5.1.4 should be presented as tables
5.1.6. Bray Curtis Cluster Analysis: not tescribed in Methods, please provide all settings and programs
Li 227: "differences between the two groups was 227 significant (R=0.37; P= 0.008)" Explain what R is here, usually this is a correlation coefficient.
Li 233 Figure 4: this is hierarchical cluster plot, not Multi-dimensional scaling (MDS) as indicated

Discussion: Li 259, "the maximum estimates of biology" is unclear

Comments on the Quality of English Language

See above

Author Response

Thank you for taking time to review this manuscript Comments 1: I am not convinced by a presentation of results and invite authors to resubmit the Ms after collecting a more sound dataset.

Response 1: [I do not understand this comment. This is a chapter from my thesis, perherps the missing information is part of the other chapters. please feel free to request additional information.

Comments 2: [My main concern is linked to a quality of material: only tree repeated experiments for each setting coupled with a little studied volume. This finally resulted in a number of different results under each setting called "outliers".????????

Response 2: Like I pointed out in my previous response, everything is available on request.   Comments 3: [In addition, preparation of the Ms is inaccurate: many references are missing, section numbering is not consistent, language is  not variable ("conducted" used 11 times) and sometimes unclear ("increases in the biology"). Other comments are below.   Response 3: Agree. I/We have revised the manuscript, section numbering rectified and have rewritten some parts of the manuscript for clearance.    Comments 4: [Abstract: needs significant linguistic revision: "increases in the biology", etc.     Response 4: Agree.  The abstract has been updated and rewritten to improve understanding (line 13 – 24)     Comments 5: [Intro: Li 28-29, "Ecosystem engineers are organisms that change th+e state of matter, both biotic and abiotic, by alter-28 ing their environments through bioturbation" Not only through bioturbation!   Response 5:  I agree; we have updated this statement to make this point clearer. The statement was rewritten (Line 28 – 30).       Comments 6: Li 96: please clarify what"macronutrients" are     Response 6: Agree. For better comprehension, I have elaborated on what macronutrients are (line 99 – 102).     Comments 7: Salinity and temperature annual variations within the Kasouga Estuary are needed here. I wonder why "Kasouga Estuary supports low levels of phytoplankton and zooplankton biomass" but "benthic communities in TOCEs typically include diverse macrofaunal and meiofaunal assemblages" and "microphytobenthic communities, such as benthic diatoms, also play a significant role in primary production nutrient cycling" That is the trophic basis for that?     Response 7: If you read the sentence from the beginning, it states that “Compared to permanently open estuaries in the region” Kasouga Estuary supports low levels of phytoplankton (line 102 – 104). So, the numbers are low only when compared to permanently open estuaries of the same region.     Comments 8: Materials and Methods: Li 115 "conducted ranged from 5 to 36 and m-2" ind per sq m?     Response 8: Agree. The typo in this statement has been corrected and m2 changed to ind/m2 ( Line 125).       Comments 9: 122 what is "standard length"?     Response 9: standard length (SL) is the distance from the tip of the rostrum (head) to the end of the last abdominal segment, excluding the telson (line 132)       Comments 10: Results: Li 167-169 move to Methods   Response 10: Agree, line 167 – 169 (formerly) was moved to Methods (Line 119– 121)   Comments 11: Four section 5.1.1 - 5.1.4 should be presented as tables   Response: Section 4.1 – 4.4 (formerly 5.1.1 – 5.1.4 has been presented as tables in the supplementary materials (Page 15 & 16).   Comments 12: 5.1.6. Bray Curtis Cluster Analysis: not tescribed in Methods, please provide all settings and programs   Response 12: Bray Curtis cluster Analysis has now been included in the Methodology and described in detail (Line 170 – 172).        Comments 13: Li 227: "differences between the two groups was 227 significant (R=0.37; P= 0.008)" Explain what R is here, usually this is a correlation coefficient.     Response 13: R in this context is called the "ANOSIM test statistic" or simply the "R-statistic" not the correlation coefficient. ANOSIM R measures the degree of separation between predefined groups based on ranked dissimilarities from Bray-Curtis similarity while “Correlation coefficient R” measures the strength and direction of a linear (Pearson) or monotonic (Spearman) relationship between two continuous variables (Line 220).     Comments 14:  Li 233 Figure 4: this is hierarchical cluster plot, not Multi-dimensional scaling (MDS) as indicated   Response: Agree.The figure caption has been revised accordingly. Changed from MDS to Hierarchical cluster plot, showing Bray-Curtis similarity (Line 222 – 223).       Comments 15: Discussion: Li 259, "the maximum estimates of biology" is unclear   Response 15: Agree. This statement has been revised (Line 247 – 249).

4. Response to Comments on the Quality of English Language

Point 1:

Response 1:

5. Additional clarifications Other changes made to the manuscript are also highlighted in RED.

 

 

 

Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

Evaluation of the manuscript "Sand prawns mitigate the impact of prolonged drought on the 2 biology of a temporary open/closed estuary" of Yekani1 & Froneman

The authors report the findings of a valuable study about the role of sand prawn (Callichirus kraussi) as an ecosystem engineer species. In a caging experiment during a prolonged drought they demonstrated that at intermediate densities the burrowing activities of sand prawn increased the microphytobenthic algal concentrations and also increased the abundance and biomass of the macrofauna.

 

In the "Statistical analysis" you write that MDS was used. It provides a scatterplot of the samples. But Figure 4 is a hierarchical tree diagram. You should clarify how the cluster (tree) diagram was created.

 

Figure 4 provides a tree diagram. MDS analysis result in a scatterplot. Something looks wrong here. At least you should change the figure legend like "Hierarchical cluster plot showing Bray-Curtis similarity . . ."

 

line 253: "[48;Error! Reference source not found.;49; 50;51]." Please correct it. There are a few similar error elsewhere in the manuscript. Please correct them. Moreover, I think that the literature it too voluminous. References includes 61 items. I propose to reduce the cited literature.

Author Response

Thank you very much for taking the time to review this manuscript. Please find the detailed responses below and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files.

Comments 1: In the "Statistical analysis" you write that MDS was used. It provides a scatterplot of the samples. But Figure 4 is a hierarchical tree diagram. You should clarify how the cluster (tree) diagram was created.

Response 1: [ Thank you for pointing this out. I/We agree with this comment. Therefore, I/we have removed MDS on the manuscript and wrote hierarchical cluster showing Bray Curtis similarity. I have included the details on the methodology section under statistical analysis.  (Line 170 – 172) under section 3.4. Statistical Analysis.

Comments 2: [Figure 4 provides a tree diagram. MDS analysis result in a scatterplot. Something looks wrong here. At least you should change the figure legend like "Hierarchical cluster plot showing Bray-Curtis similarity .]

Response 2: Agree. I/We have changed the figure legend and captioned it as "Hierarchical cluster plot showing Bray-Curtis similarity. Line (222 – 223)   Comments 3: [line 253: "[48;Error! Reference source not found.;49; 50;51]." Please correct it. There are a few similar error elsewhere in the manuscript. Please correct them. Moreover, I think that the literature it too voluminous. References includes 61 items. I propose to reduce the cited literature].   Response 3: Agree. I/We have amended this throughout the manuscript.

4. Response to Comments on the Quality of English Language

Point 1:

Response 1: (in red)

5. Additional clarifications Other changes made to the manuscript have also been highlighted in red.

 

 

 

Author Response File: Author Response.docx

Reviewer 3 Report

Comments and Suggestions for Authors

This manuscript presents potentially interesting research, however, due to several issues and inaccuracies, it cannot be accepted in its current form. I have provided a series of comments to help improve the manuscript and sincerely hope the authors will consider these suggestions.

Introduction

The introduction is generally well-structured, but the following points require attention:

1. I would recommend avoiding the citation of a master's thesis as the primary reference for defining terms such as bioturbation or ecological engineering (line 29). More authoritative sources are available. For bioturbation, I suggest citing Kristensen et al. 2012 (doi: 10.3354/meps09506), and for ecosystem engineering, Romero et al. 2015 (doi: 10.1111/brv.12138).
2. Regarding your model species, recent taxonomic revisions by Poore et al. 2019 (doi: 10.24199/j.mmv.2019.78.05) have reclassified this species based on genetic evidence from Callichirus to the newly established genus Kraussillichirus. Consequently, the correct name should be Kraussillichirus kraussi (Stebbing, 1900). Please revise this throughout the manuscript, starting from line 53 (and in the Abstract). Should you disagree with this taxonomic update, kindly provide a brief justification.
3. In line 62, the statement that sand prawns contribute to "the displacement of non-living organisms" is unclear. If you are referring to "dead" organisms, please specify this explicitly for clarity.
4. Please verify the citation of paper no. 29 on the impact of sand extraction on benthic ecosystems (line 74) to confirm whether sand prawns are indeed reported to "promote biodiversity by creating habitats that are more favorable to certain species."
5. While you present the general aim of your study, it would be beneficial to outline specific research objectives. Ideally, these should be framed as testable hypotheses.

Study Site

1. There appears to be no reference to Fig. 1 in this section. Please ensure this figure is appropriately cited where relevant.
2. For species names, it is standard practice to include taxonomic authorities upon their first mention. For instance, line 99 could be revised to Pseudodiaptomus hessei (Mrázek) and Paracartia longipatella (Connell & Grindley). If you agree with this convention, please apply it consistently throughout the manuscript.

Materials and Methods

1. In lines 113–114, you state: “Manipulations were conducted over a period of three months from 1 January to 15 March 2020.” However, this timeframe actually covers two and a half months, not three. Furthermore, since sand prawns were introduced “three weeks after installing the cages” (line 121), the impact of sand prawns on bioturbation, benthic algae, and macrofauna was effectively tested over a shorter duration of approximately one month and three weeks. Could you clarify why sand prawns were added three weeks after cage installation rather than on the same day?
2. Ensure consistent notation for Chlorophyll a concentration throughout the manuscript. In line 144, it is written as "Chl-a," while in line 147 it appears as "Chl a." Please standardize this notation consistently.
3. In Subchapter “3.1.3 Epifauna and infauna community structure” (lines 148–156), you describe the methods for assessing total abundance and biomass of epi- and infauna and the identification key used. However, it is unclear how the community structure was described and analyzed (e.g., what indices were employed). Please provide this missing information.
4. The chapter “4. Statistical analyses” (lines 157–165) lacks several crucial details: a) Specify what aspects you tested for significant differences between treatments using one-way ANOVA. Were these differences evaluated in terms of a bioturbation rates, microphytobenthic algal concentration, epi- and infaunal abundance, and epi- and infaunal biomass? b) Since ANOVA is a parametric method, it is essential to explain how you assessed whether its assumptions (normality and homoscedasticity) were met to ensure the reliability of results. c) Although Simpson’s diversity index is mentioned, no corresponding results appear in the Results section. Please either include this analysis in the Results or remove mention of the index from the Materials and Methods section. d) For Non-metric Multi-Dimensional Scaling (MDS), you need to specify the similarity or dissimilarity index used and the type of data matrix (e.g., raw or transformed abundances, presence/absence). Although the Results section (line 223) mentions the use of Bray-Curtis similarity, MDS itself was not applied, and instead, a cluster analysis was performed. Ensure consistency by accurately describing the method used. If you opt to retain the cluster analysis, provide detailed information, including the clustering algorithm employed (e.g., single linkage, Ward’s, UPGMA), the similarity index used, and any constraints applied, if necessary. e) The use of ANOSIM to test differences in community structure and composition between control and sand prawn treatments is appropriate. However, I do not follow the rationale for testing differences between groupings generated by the cluster analysis. Clusters that combine replicates from different treatments may not hold clear biological meaning. Please clarify the biological significance of these groupings or reconsider the relevance of this approach.

Results

This section is poorly written and contains numerous errors and deficiencies. It lacks essential raw data, which prevents reviewers and prospective readers from independently interpreting the findings or evaluating the validity of the methods used. I strongly recommend that the authors provide tables containing raw data for bioturbation, algal concentration, and macrofaunal abundance and biomass for each replicate under all experimental treatments and control conditions. These tables could be included as supplementary material to avoid adding bulk to the main article. Additionally, it would be helpful to include species-level raw abundance data for both epifauna and infauna within each cage to better assess the dataset's completeness and robustness.

Below are specific points requiring correction and clarification:

1. The statistical analysis results for bioturbation rates (lines 175–179) are inconsistent with what is depicted in Fig. 2a. In Fig. 2a, different letters ("a" to "d") denote statistically significant differences between each treatment and the control. However, the text states: “ANOVA indicated that the bioturbation rates in Treatments 2 and 3 were significantly higher than those recorded in the Control and Treatment 1 (F = 29.78; P < 0.001). There were no significant differences in the bioturbation rates between Treatment 2 and Treatment 3 (P > 0.05). Similarly, the bioturbation rates in the Control and Treatment 1 were not significantly different from one another (P > 0.05).” Please reconcile these discrepancies between the textual description and the figure. Furthermore, the textual results often redundantly restate information presented in figures, such as Fig. 2a. Instead, textual descriptions should complement figures by providing additional insights rather than repeating visual data. This suggestion applies throughout the Results section.
2. Similar inconsistencies appear in other subsections of the Results (5.1.2, 5.1.3, and 5.1.4) in relation to Fig. 2. For instance, lines 186–187 state: “ANOVA revealed that there was a significant difference between all treatment groups (F = 3.48; P < 0.05).” However, Fig. 2b shows Treatment 1 as “ab,” indicating no significant difference between the control and Treatment 1, or between Treatment 1 and Treatment 2. Given the high variability (SD) in the control, Treatments 2, and 3, significant differences in Chl-a concentration between these treatments seem unlikely. These inconsistencies undermine confidence in the results and must be addressed.
3. The whisker lengths in Fig. 2b for Treatment 1 do not correspond to the value provided in line 183 (SD = 0.61), which is almost equal to the treatment's mean value (0.627). Please correct this discrepancy.
4. In subsections 5.1.3 and 5.1.4, macrofaunal abundance and biomass are reported as individuals m^-³ and mg wwt m^-³, respectively. This unit implies that only infauna was analyzed. What about epifauna (abundance of what should be expressed as ind m^-2)? Please clarify whether epifauna were excluded or provide appropriate units.
5. Line 180: Correct “18 ind” to “180 ind”.
6. Lines 193–195: The authors conclude: “The total macrobenthic abundances did not differ significantly between the Control and the various treatments.” However, the ANOVA result provided is F = 6.7, P = 0.006. This clearly indicates significant differences. Please revise this statement accordingly.
7. Line 200: The reported SD for Treatment 2 (0.508) does not match the whisker length in Fig. 2d, which suggests a much larger value (at least 2). Please correct this inconsistency.
8. Lines 201–203: Another inconsistency between text and Fig. 2d is evident. The figure suggests that Treatment 1 should not differ significantly from the control, given that it shows no significant differences from Treatments 2 and 3. Please address this issue.
9. Fig. 2: In the Y-axis titles, replace the caret symbol (^) with “-1” to indicate units correctly. The caret is typically used for exponentiation and may confuse readers.
10. Subchapter “5.1.5 Epifaunal and infaunal community structure” (lines 210–218) is poorly presented. The repeated reference to “the epifaunal species” makes it unclear which species are categorized as epifauna versus infauna. It would be clearer to list recorded species (with their authorities) and their abundances in a table rather than using Fig. 3, which is difficult to interpret for species with low densities due to the linear Y-axis scale. A log scale may improve readability. Moreover, Fig. 3 is not referenced in the text. The conclusion that “There were no significant differences in the community structure of epifaunal and infaunal species” seems implausible, given the extremely low probability value (P = 1.13E-23). The test used is not specified. Please clarify the method employed and explain whether epifauna and infauna were treated as a combined community or analyzed separately, as inconsistencies appear between the Results and Methods sections.
11. Fig. 3: a) Ensure consistent treatment labeling throughout the manuscript. In Fig. 3, the control is labeled as Treatment 1, while Treatment 1 becomes Treatment 2, and so forth. b) Clarify the meaning of the category “AN other.” How many species does it represent? This grouping is problematic, as its abundance is relatively high in Treatment 1. c) Replace “density” with “abundance” in the Y-axis title and caption to align with the terminology in the Methods section. d) Either omit treatment descriptions in the caption or specify that the number per square meter in each treatment refers to sand prawns.
12. Subchapter “5.1.6 Bray-Curtis Cluster Analysis” (lines 223–244): a) Line 223: The cluster analysis is not described in the Methods section. This is the first mention of the Bray-Curtis similarity index, please include this information in the Methods section. b) Line 224: Seven clusters (including an outlier) are visible at a 70% similarity level, not just two groups as claimed. The two groups emerge at the 60% similarity level. c) Line 226: Group 2 includes samples from the control and all three treatments, not just Treatments 2 and 3 as erroneously stated. The authors also incorrectly reference Fig. 5, which does not exist, instead of Fig. 4. d) Line 227: Correct the grammar to “differences (…) were.” e) Cluster analysis may not be the best approach for this study. An MDS plot would better visualize overall variation in the multivariate dataset, while differences should be tested using a robust multivariate method such as ANOSIM or PERMANOVA between treatments rather than relying on cluster groupings. f) Clarify whether epifauna and infauna were combined or treated separately. g) Fig. 4 caption: MDS and cluster analysis are distinct methods. Correct the caption to say "Hierarchical cluster plot." This figure presents a cluster analysis, not an MDS plot. h) Table 1: This table is not referenced in the text. The caption requires grammatical improvement and clarification regarding whether epifauna and infauna were combined. The SIMPER analysis should be described in the Methods section and applied to the predefined treatments rather than cluster groupings. Additionally, please format the table properly, including consistent decimal places and clearer species names (e.g., by wrapping text in cells). i) Line 244 should delete the value "19.9%" as it duplicates information from the previous sentence about P. laticeps.

Discussion

This section is reasonably developed but will require modifications after the necessary corrections to analyses and interpretations highlighted in my previous notes. Additionally, I recommend addressing the following points:

1. Line 249: Reference no. 44 pertains to ecosystems in New Zealand, yet it is cited concerning South African estuaries. Please provide an appropriate reference specific to South Africa or explain the relevance of the New Zealand study.
2. Lines 259–260: The phrase "maximum estimates of biology" is unclear. Please clarify what this refers to, whether it concerns biomass, productivity, or some other metric.
3. Line 271: While this aligns with Fig. 2c, it contradicts the results presented in lines 177–179. Please ensure consistency between textual descriptions and graphical data.
4. Line 273: The correct reference here should be Figure 2b, not Figure 1(b).
5. Lines 279–282: Could you provide a potential explanation for why treatments with 10 and 20 sand prawns appear to bury algae, whereas the 5-prawn treatment seemingly enhances macronutrient availability?
6. Line 285: Figures 2c and 2d should be referenced here instead of Figures 3 and 4.
7. Line 301: The control is typically used as a baseline or reference condition. Clarify what is meant by elevated algae concentrations in the control. Elevated compared to what?
8. Line 302: Figure 2 should be referenced here instead of Figure 1, and there are no Figures 5 or 6 in this manuscript.
9. Line 309: Specify what "production declines" refer to—whether this pertains to algal biomass, macrobenthic abundance, or some other factor.

Conclusion

The conclusion lacks evidence if any significant differences in macrofauna community structure and composition was demonstrated between the control and experimental treatments.

Edits

Numerous deficiencies require attention. Below are examples, but the entire manuscript should be carefully reviewed and edited:

1. Section Numbering and Headings: a) The numbering and formatting of headings are inconsistent. b) The second-level subsection under "Materials and Methods" should be "3.1 Bioturbation," not "3.1.1". c) The section titled "Statistical analysis" should be included under "Materials and Methods" and numbered as "3.4". d) The full-stop usage in second- or third-level subsection numbers is inconsistent. For example, "5.1.1." includes a full stop at the end, while earlier sections do not “3.1.1”. e) Discussion and Conclusion have the same number (6).
2. Citations: a) Ensure consistency in citation styles. In some places, citations are separated by commas (e.g., line 29), while semicolons are used elsewhere (e.g., line 38). b) References should follow ascending numerical order (e.g., line 38). c) Check for missing or incorrect references (e.g., line 70, references nos. 26 or 32).
3. Spacing: a) Maintain consistent spacing between numbers and units (e.g., compare line 56 vs. line 98). b) Ensure spaces before and after mathematical symbols (e.g., "P> 0.05" in line 178 should read "P > 0.05").
4. Punctuation: a) Line 55: Full stop incorrectly appears before the citation. b) Line 156: Double full stops at the end of the sentence. c) Line 138: Missing full stop. d) Lines 175 and 184: Unnecessary spaces before punctuation. e) Lines 228 and 230: Unnecessary full stops between the genus and species names.
5. Typographical Errors: a) Line 99: Delete the first "and." b) Line 115: Correct "and" to "ind." c) Line 398: Split "idiosyncraticeffects" into two words. d) Line 417: Correct capitalization for geographical names.
6. Species Names: Ensure that species names in the reference titles are written in italics for consistency.

Author Response

Thank you very much for taking the time to review this manuscript. Please find the detailed responses below and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files.

Comments 1: [The introduction is generally well-structured, but the following points require attention:I would recommend avoiding the citation of a master's thesis as the primary reference for defining terms such as bioturbation or ecological engineering (line 29). More authoritative sources are available. For bioturbation, I suggest citing Kristensen et al. 2012 (doi: 10.3354/meps09506), and for ecosystem engineering, Romero et al. 2015 (doi: 10.1111/brv.12138).

Response 1: Thank you for pointing this out. I/We agree with this comment. Therefore, I/we have [inserted Kristensen et al. 2012 as reference number 6 (line 32) and updated in the reference list ( line 478-479) in the manuscript]

Comments 2: [Regarding your model species, recent taxonomic revisions by Poore et al. 2019 (doi: 10.24199/j.mmv.2019.78.05) have reclassified this species based on genetic evidence from Callichirus to the newly established genus Kraussillichirus. Consequently, the correct name should be Kraussillichirus kraussi (Stebbing, 1900). Please revise this throughout the manuscript, starting from line 53 (and in the Abstract). Should you disagree with this taxonomic update, kindly provide a brief justification.

Response 2: Agree. I/We have, accordingly, done/revised/changed/modified to emphasize this point. The species name has been updated from from Callichirus kraussi to the newly established genus Kraussillichirus kraussi throughout the manuscript         Comments 3: In line 62, the statement that sand prawns contribute to "the displacement of non-living organisms" is unclear. If you are referring to "dead" organisms, please specify this explicitly for clarity.   Response: I/We have revised the statement accordingly, to emphasize this point (see line 61 – 64).     Comments 4: Please verify the citation of paper no. 29 on the impact of sand extraction on benthic ecosystems (line 74) to confirm whether sand prawns are indeed reported to "promote biodiversity by creating habitats that are more favorable to certain species."   Response: Agree. I/We have, modified the citation to emphasize this point. Citation was removed (line 74)     Comments 5: While you present the general aim of your study, it would be beneficial to outline specific research objectives. Ideally, these should be framed as testable hypotheses.   Response: Agree. I/We have revised the manuscript to emphasize this point. Hypothesis has been included in the manuscript (line 85 – 88).     Comments 6: [There appears to be no reference to Fig. 1 in this section. Please ensure this figure is appropriately cited where relevant]. Response: [The figure was referenced after the caption (please see line 115, previously line 108]       Comments 7: [For species names, it is standard practice to include taxonomic authorities upon their first mention. For instance, line 99 could be revised to Pseudodiaptomus hessei (Mrázek) and Paracartia longipatella (Connell & Grindley). If you agree with this convention, please apply it consistently throughout the manuscript].   Response: Agree and thank you for pointing this out. I/We have effected these changes accordingly throughout the manuscript, to emphasize this point. Taxonomic authorities for species have been included [line 105 – 109].     Comments 8: In lines 113–114, you state: “Manipulations were conducted over a period of three months from 1 January to 15 March 2020.” A. However, this timeframe actually covers two and a half months, not three. B. Furthermore, since sand prawns were introduced “three weeks after installing the cages” (line 121), the impact of sand prawns on bioturbation, benthic algae, and macrofauna was effectively tested over a shorter duration of approximately one month and three weeks. C. Could you clarify why sand prawns were added three weeks after cage installation rather than on the same day?   Response: A. Agree. I/We have, changed the duration of the study to emphasize this point. Timeframes have been amended to 2 and a half months ( line 123). A statement to clarify why sand prawns were added three weeks after cage installation rather than on the same day was included in the text (line 133 - 134).   Comments 9: Ensure consistent notation for Chlorophyll a concentration throughout the manuscript. In line 144, it is written as "Chl-a," while in line 147 it appears as "Chl a." Please standardize this notation consistently.   Response: Agree. I/We have done this accordingly. Chl a was changed to Chl-a throughout the manuscript (line 159)   Comments 10: In Subchapter “3.1.3 Epifauna and infauna community structure” (lines 148–156), you describe the methods for assessing total abundance and biomass of epi- and infauna and the identification key used. However, it is unclear how the community structure was described and analyzed (e.g., what indices were employed). Please provide this missing information?????   Response: Agree, and thank you for pointing this out I/We have, removed this section from the manuscript for further analysis.       Comments 11: The chapter “4. Statistical analyses” (lines 157–165) lacks several crucial details: a) Specify what aspects you tested for significant differences between treatments using one-way ANOVA done. Were these differences evaluated in terms of a bioturbation rates, microphytobenthic algal concentration, epi- and infaunal abundance, and epi- and infaunal biomass? b) Since ANOVA is a parametric method, it is essential to explain how you assessed whether its assumptions (normality and homoscedasticity) were met to ensure the reliability of results. c) Although Simpson’s diversity index is mentioned, no corresponding results appear in the Results section. Please either include this analysis in the Results or remove mention of the index from the Materials and Methods section. d) For Non-metric Multi-Dimensional Scaling (MDS), you need to specify the similarity or dissimilarity index used and the type of data matrix (e.g., raw or transformed abundances, presence/absence) ????. Although the Results section (line 223) mentions the use of Bray-Curtis similarity, MDS itself was not applied, and instead, a cluster analysis was performed. Ensure consistency by accurately describing the method used. If you opt to retain the cluster analysis, provide detailed information, including the clustering algorithm employed (e.g., single linkage, Ward’s, UPGMA), the similarity index used, and any constraints applied, if necessary. e) The use of ANOSIM to test differences in community structure and composition between control and sand prawn treatments is appropriate. However, I do not follow the rationale for testing differences between groupings generated by the cluster analysis. Clusters that combine replicates from different treatments may not hold clear biological meaning. Please clarify the biological significance of these groupings or reconsider the relevance of this approach ???. Results.   Response: Agree. I/We have, revised the statistical analysis, post hoc turkey test was conducted to ensure the reliability of the results.  I/We re-wrote the entire section for statistical analysis (line 167 – 177), removed any mention of diversity as well as MDS.     Comments 12: This section is poorly written and contains numerous errors and deficiencies. It lacks essential raw data, which prevents reviewers and prospective readers from independently interpreting the findings or evaluating the validity of the methods used. I strongly recommend that the authors provide tables containing raw data for bioturbation, algal concentration, and macrofaunal abundance and biomass for each replicate under all experimental treatments and control conditions. These tables could be included as supplementary material to avoid adding bulk to the main article. Additionally, it would be helpful to include species-level raw abundance data for both epifauna and infauna within each cage to better assess the dataset's completeness and robustness.   Response 12: [Agree. The raw data has been supplied in the form of tables as supplementary materials as suggested, Page 16 &17].     Comments 13: The statistical analysis results for bioturbation rates (lines 175–179) are inconsistent with what is depicted in Fig. 2a. In Fig. 2a, different letters ("a" to "d") denote statistically significant differences between each treatment and the control. However, the text states: “ANOVA indicated that the bioturbation rates in Treatments 2 and 3 were significantly higher than those recorded in the Control and Treatment 1 (F = 29.78; P < 0.001). There were no significant differences in the bioturbation rates between Treatment 2 and Treatment 3 (P > 0.05). Similarly, the bioturbation rates in the Control and Treatment 1 were not significantly different from one another (P > 0.05).” Please reconcile these discrepancies between the textual description and the figure. Furthermore, the textual results often redundantly restate information presented in figures, such as Fig. 2a. Instead, textual descriptions should complement figures by providing additional insights rather than repeating visual data. This suggestion applies throughout the Results section.   Response: Agree. I/We have modified and re-wrote this section to correct these  inconsistencies (line 181 – 187).   Comments 14: Similar inconsistencies appear in other subsections of the Results (5.1.2, 5.1.3, and 5.1.4) in relation to Fig. 2. For instance, lines 186–187 state: “ANOVA revealed that there was a significant difference between all treatment groups (F = 3.48; P < 0.05).” However, Fig. 2b shows Treatment 1 as “ab,” indicating no significant difference between the control and Treatment 1, or between Treatment 1 and Treatment 2. Given the high variability (SD) in the control, Treatments 2, and 3, significant differences in Chl-a concentration between these treatments seem unlikely. These inconsistencies undermine confidence in the results and must be addressed. Response: Agree. I/We have modified and re-wrote these results to address these conflicting statements, subsection 4.2 – 4.4 (line 189 – 207)].       Comments 15: The whisker lengths in Fig. 2b for Treatment 1 do not correspond to the value provided in line 183 (SD = 0.61), which is almost equal to the treatment's mean value (0.627). Please correct this discrepancy.   Response: Agree. I/We have changed the SD to SE to show variability between sample means (lines 212).   Comments 16: In subsections 5.1.3 and 5.1.4, macrofaunal abundance and biomass are reported as individuals m-³ and mg wwt m-³, respectively. This unit implies that only infauna was analyzed. What about epifauna (abundance of what should be expressed as ind m-2)? Please clarify whether epifauna were excluded or provide appropriate units.   Response: Agree. I/We have, accordingly, done/revised/changed/modified to emphasize this point, biomass was reported as grams wet weight per square meter (g wwt/m²) to account for both infaunal and epifaunal organisms (Figure 2).   Comments 17: Line 180: Correct “18 ind” to “180 ind”.   Response: Agree. I/We have corrected these mistakes and rewrote this section (line 196 – 202).    Comments 18: Lines 193–195: The authors conclude: “The total macrobenthic abundances did not differ significantly between the Control and the various treatments.” However, the ANOVA result provided is F = 6.7, P = 0.006. This clearly indicates significant differences. Please revise this statement accordingly.   Response: Agree. The mistake has been rectified and this section was revised, no significant differences was changed to significantly different (line 200).   Comments 19: Line 200: The reported SD for Treatment 2 (0.508) does not match the whisker length in Fig. 2d, which suggests a much larger value (at least 2). Please correct this inconsistency.   Response: Agree. I/We have revised the whisker length accordingly. SE was used to show variability between sample means instead of SD (line 212)     Comments 20: Lines 201–203: Another inconsistency between text and Fig. 2d is evident. The figure suggests that Treatment 1 should not differ significantly from the control, given that it shows no significant differences from Treatments 2 and 3. Please address this issue.   Response: Agree. The inconsistency between text and figure has been addressed and revised to emphasize this point. (Line 204 to 207)   Comments 21: Fig. 2: In the Y-axis titles, replace the caret symbol (^) with “-1” to indicate units correctly. The caret is typically used for exponentiation and may confuse readers.   Response: Agree. I/We have replaced the symbol ^ with an exponential 1 to avoid further confusion (figure 2).   Comments 22: Subchapter “5.1.5 Epifaunal and infaunal community structure” (lines 210–218) is poorly presented. The repeated reference to “the epifaunal species” makes it unclear which species are categorized as epifauna versus infauna. It would be clearer to list recorded species (with their authorities) and their abundances in a table rather than using Fig. 3, which is difficult to interpret for species with low densities due to the linear Y-axis scale. A log scale may improve readability. Moreover, Fig. 3 is not referenced in the text. The conclusion that “There were no significant differences in the community structure of epifaunal and infaunal species” seems implausible, given the extremely low probability value (P = 1.13E-23). The test used is not specified. Please clarify the method employed and explain whether epifauna and infauna were treated as a combined community or analyzed separately, as inconsistencies appear between the Results and Methods sections.   Response: Agree. The section has been removed from the manuscript for careful analysis and write up.   Comments 23: Fig. 3: a) Ensure consistent treatment labeling throughout the manuscript. In Fig. 3, the control is labeled as Treatment 1, while Treatment 1 becomes Treatment 2, and so forth. b) Clarify the meaning of the category “AN other.” How many species does it represent? This grouping is problematic, as its abundance is relatively high in Treatment 1. c) Replace “density” with “abundance” in the Y-axis title and caption to align with the terminology in the Methods section. d) Either omit treatment descriptions in the caption or specify that the number per square meter in each treatment refers to sand prawns.   Response: Agree. I/We have removed the figure to avoid further confusion.     Comments 24: Subchapter “5.1.6 Bray-Curtis Cluster Analysis” (lines 223–244): a) Line 223: The cluster analysis is not described in the Methods section. This is the first mention of the Bray-Curtis similarity index, please include this information in the Methods section. b) Line 224: Seven clusters (including an outlier) are visible at a 70% similarity level, not just two groups as claimed. The two groups emerge at the 60% similarity level. c) Line 226: Group 2 includes samples from the control and all three treatments, not just Treatments 2 and 3 as erroneously stated. The authors also incorrectly reference Fig. 5, which does not exist, instead of Fig. 4. d) Line 227: Correct the grammar to “differences (…) were.” e) Cluster analysis may not be the best approach for this study. An MDS plot would better visualize overall variation in the multivariate dataset, while differences should be tested using a robust multivariate method such as ANOSIM or PERMANOVA between treatments rather than relying on cluster groupings. f) Clarify whether epifauna and infauna were combined or treated separately. g) Fig. 4 caption: MDS and cluster analysis are distinct methods. Correct the caption to say "Hierarchical cluster plot." This figure presents a cluster analysis, not an MDS plot. h) Table 1: This table is not referenced in the text. The caption requires grammatical improvement and clarification regarding whether epifauna and infauna were combined. The SIMPER analysis should be described in the Methods section and applied to the predefined treatments rather than cluster groupings. Additionally, please format the table properly, including consistent decimal places and clearer species names (e.g., by wrapping text in cells). i) Line 244 should delete the value "19.9%" as it duplicates information from the previous sentence about P. laticeps.   Response: Agree. I/We have modified and re-wrote the entire Hierarchical cluster analysis section, removed MDS, changed figure caption and described the SIMPER analysis properly in methods (line 175 – 177 & 215 – 230).   Discussion     Comments 25: Line 249: Reference no. 44 pertains to ecosystems in New Zealand, yet it is cited concerning South African estuaries. Please provide an appropriate reference specific to South Africa or explain the relevance of the New Zealand study.   Response: Agree. Appropriate references have been provided and removed the New Zealand ref (line 237)     Comments 26: Lines 259–260: The phrase "maximum estimates of biology" is unclear. Please clarify what this refers to, whether it concerns biomass, productivity, or some other metric.   Response: Agree. The statement has been revised (line 246 - 248)     Comments 27: Line 271: While this aligns with Fig. 2c, it contradicts the results presented in lines 177–179. Please ensure consistency between textual descriptions and graphical data. Fix results   Response: Agree. Textual descriptions and graphical data have been modified, results section has been re-written to match text.       Comments 28: Line 273: The correct reference here should be Figure 2b, not Figure 1(b).   Response: Agree. I/We have modified this accordingly (line 259)     Comments 29: Lines 279–282: Could you provide a potential explanation for why treatments with 10 and 20 sand prawns appear to bury algae, whereas the 5-prawn treatment seemingly enhances macronutrient availability?   Response: Agree. The statement has been revised to better explain why the treatment with 5 prawns enhanced macronutrient availability that the ones with 10 and 20 sand prawns (line 256-262)     Comments 30: Line 285: Figures 2c and 2d should be referenced here instead of Figures 3 and 4.   Response: Agree. Figures 2c and 2d have been referenced in line 354 instead of 3 and 4 (Line 269).       Comments 31: Line 301: The control is typically used as a baseline or reference condition. Clarify what is meant by elevated algae concentrations in the control. Elevated compared to what?   Response: Agree. I/We have rephrased the statement accordingly (line 268 - 269)     Comments 32: Line 302: Figure 2 should be referenced here instead of Figure 1, and there are no Figures 5 or 6 in this manuscript.   Response: Agree. Figure refence has been changed from figure 1 to figure 2 and figure 5 and 6 text removed (line 283).     Comments 33: Line 309: Specify what "production declines" refer to—whether this pertains to algal biomass, macrobenthic abundance, or some other factor. Conclusion-   Response: Agree. I/We have changed the statement accordingly (line 268 - 269)   Comments 34: The conclusion lacks evidence if any significant differences in macrofauna community structure and composition was demonstrated between the control and experimental treatments.   Response: Agree. The conclusion was re-written to better emphasize the findings of the experiment (line 292 – 307)

4. Response to Comments on the Quality of English Language

Point 1: Numerous deficiencies require attention. Below are examples, but the entire manuscript should be carefully reviewed and edited     Response 1: (The entire manuscript has been reviewed and hopefully fixed all the suggested edits (Page 1 to page 18).     Point 2: Section Numbering and Headings: a) The numbering and formatting of headings are inconsistent. b) The second-level subsection under "Materials and Methods" should be "3.1 Bioturbation," not "3.1.1". c) The section titled "Statistical analysis" should be included under "Materials and Methods" and numbered as "3.4". d) The full-stop usage in second- or third-level subsection numbers is inconsistent. For example, "5.1.1." includes a full stop at the end, while earlier sections do not “3.1.1”. e) Discussion and Conclusion have the same number (6).   Response 2: a. Numbering and formatting of headings have been rectified and are now consistent. b. The subsection 3.1.1. Bioturbation has been changed to 3.1. (line 143) c. The section "Statistical analysis" was moved to "Materials and Methods" and numbered as "3.4" (line 167) d. The full-stop usage in second- or third-level subsection numbers has been fixed and now consistent. Numbers for Discussion and conclusion have been changed (lines 234 & 291).   Point 3: Citations: a) Ensure consistency in citation styles. In some places, citations are separated by commas (e.g., line 29), while semicolons are used elsewhere (e.g., line 38). b) References should follow ascending numerical order (e.g., line 38). c) Check for missing or incorrect references (e.g., line 70, references nos. 26 or 32).   Response 3: a) Citation style has been corrected (Page 10 - 14) b) All references now follow ascending numerical order (page 1 – 9) c) Incorrect and missing references have been modified (Page 1 – 9)   Point 4: Spacing: a) Maintain consistent spacing between numbers and units (e.g., compare line 56 vs. line 98). b) Ensure spaces before and after mathematical symbols (e.g., "P> 0.05" in line 178 should read "P > 0.05").   Response 4: a) Spacing between numbers and units are now fixed throughout the manuscript (page 1 to 10). b) Space before and after Mathematical symbols have been corrected where appropriate.      Point 5: Punctuation: a) Line 55: Full stop incorrectly appears before the citation. b) Line 156: Double full stops at the end of the sentence. c) Line 138: Missing full stop. d) Lines 175 and 184: Unnecessary spaces before punctuation. e) Lines 228 and 230: Unnecessary full stops between the genus and species names.   Response 5: a) Full stop removed before citation b) Second full stop removed at the end of the sentence in   Point 6: Typographical Errors: a) Line 99: Delete the first "and." b) Line 115: Correct "and" to "ind." c) Line 398: Split "idiosyncraticeffects" into two words. d) Line 417: Correct capitalization for geographical names.   Response 6: a) ‘’and’’ deleted in line b) and changed to ind c) idiosyncratic effect has been split into two words d) Geographical names have been capitalized     Point 7: Species Names: Ensure that species names in the reference titles are written in italics for consistency Response 7: a) All species name have been written in italics in the references and throughout the manuscript.       5. Additional clarifications Other changes made to the manuscript have also been highlighted in red.

 

 

 

 

 

 

 

 

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The text has been sufficiently improved, whereas my main previous concern - a poorly representative dataset resulting in outliers - remain unaddressed. In addition, I could not see itemized answers to my comments. In this case my choice is not too rich- to recommend either rejection or acceptance of the paper in its present form. I choose acceptance and invite the authors to base their future papers on more representative dataset (see my recommendation in the previous review).

Author Response

We sincerely appreciate the time and effort you have dedicated to reviewing our manuscript. Below, we provide detailed responses to each of your comments, with corresponding revisions clearly highlighted in red in the resubmitted files. Thank you again for your valuable feedback.

Comments and Suggestions for Authors

The text has been sufficiently improved, whereas my main previous concern - a poorly representative dataset resulting in outliers - remain unaddressed. In addition, I could not see itemized answers to my comments. In this case my choice is not too rich- to recommend either rejection or acceptance of the paper in its present form. I choose acceptance and invite the authors to base their future papers on more representative dataset (see my recommendation in the previous review).

Response: We sincerely appreciate the reviewer’s thorough evaluation and their decision to recommend acceptance of our manuscript. We acknowledge the concern regarding the representativeness of our dataset and the presence of outliers. As noted in our previous response, our study was conducted under natural field conditions, where environmental variability is inherent, particularly in dynamic estuarine systems. While we recognize the limitations of our dataset, we believe it still provides valuable insights into the role of Kraussillichirus kraussi in ecosystem resilience during drought conditions.

Moving forward, we will take the reviewer’s recommendation into account and aim to expand our dataset in future studies to enhance its representativeness. Additionally, we apologize if our itemized responses were unclear or difficult to locate. We have ensured that all reviewer comments were addressed in our point-by-point response, but we are happy to provide further clarification if needed. Once again, we appreciate the constructive feedback, which has helped improve our manuscript, and we thank the reviewer for their time and consideration.

Reviewer 3 Report

Comments and Suggestions for Authors

I have reviewed the revised manuscript and acknowledge that several of my previous comments have been addressed. However, there are still significant shortcomings that need to be corrected before the paper can be accepted. I have provided additional comments (marked as NEW COMMENT) in the relevant sections, following my original comments and the authors’ responses. I have omitted points that have already been adequately addressed.

 

Original Comment 6: There appears to be no reference to Fig. 1 in this section. Please ensure this figure is appropriately cited where relevant.

Response: The figure was referenced after the caption (please see line 115, previously line 108].

NEW COMMENT 1:

There is still no explicit reference to Figure 1 within the "Study Site" section or elsewhere in the manuscript, as was also the case in the original submission. The only mention of this figure is in the caption (lines 115–116, previously lines 108–109), but it is not cited in the text. Please ensure that Figure 1 is appropriately referenced in the main text. Additionally, the citation in the figure caption, which refers to the source of the map (i.e., Froneman, 2013), should be formatted numerically rather than by author name and year.

 

Original Comment 7: For species names, it is standard practice to include taxonomic authorities upon their first mention. For instance, line 99 could be revised to Pseudodiaptomus hessei (Mrázek) and Paracartia longipatella (Connell & Grindley). If you agree with this convention, please apply it consistently throughout the manuscript.

Response: Agree and thank you for pointing this out. I/We have effected these changes accordingly throughout the manuscript, to emphasize this point. Taxonomic authorities for species have been included [line 105 – 109].

NEW COMMENT 2:

Thank you for adding taxonomic authorities; however, they should not be italicized, unlike species names. Please ensure that taxonomic authorities are presented in plain text. Additionally, species collected during the study still lack taxonomic authorities (see page 8, lines 224–225, as well as Table 1 and the final unnumbered table in the Supplementary Material), leading to inconsistency in the manuscript. I strongly recommend including taxonomic authorities for species names in both tables. This would eliminate the need to repeatedly provide taxonomic authorities for collected species throughout the text.

 

Original Comment 10: In Subchapter “3.1.3 Epifauna and infauna community structure” (lines 148–156), you describe the methods for assessing total abundance and biomass of epi- and infauna and the identification key used. However, it is unclear how the community structure was described and analyzed (e.g., what indices were employed). Please provide this missing information.

Response: Agree, and thank you for pointing this out I/We have, removed this section from the manuscript for further analysis.

NEW COMMENT 3:

The section now titled “3.3. Macrofaunal Community” remains in the revised manuscript. If you have not provided methods for analyzing community structure, I recommend modifying the phrase in line 161 from “The macrofaunal community structure…” to “The macrofaunal abundance, biomass, and community composition…” to align with the description in lines 140–141. Additionally, please clearly indicate (as done in subsections 3.1. and 3.2.) that macroinvertebrate abundance and biomass are expressed as the number of individuals per m³ and mg wet weight per m³, respectively.

However, I would argue that since cluster analysis and SIMPER were employed, you have, in fact, analyzed macrofaunal community structure. Moving the description of these methods—specifically, cluster analysis (which should explicitly mention the similarity index used, i.e., Bray–Curtis)—from subsection “3.4. Statistical Analysis” to section “3.3. Macrofaunal Community” would better reflect your approach. This restructuring would also improve logical flow, as cluster analysis and SIMPER are not strictly statistical methods. However, please also refer to my concerns in NEW COMMENT 4e.

 

Original Comment 11: The chapter “4. Statistical analyses” (lines 157–165) lacks several crucial details: a) Specify what aspects you tested for significant differences between treatments using one-way ANOVA done. Were these differences evaluated in terms of a bioturbation rates, microphytobenthic algal concentration, epi- and infaunal abundance, and epi- and infaunal biomass?

1. b) Since ANOVA is a parametric method, it is essential to explain how you assessed whether its assumptions (normality and homoscedasticity) were met to ensure the reliability of results.
2. c) Although Simpson’s diversity index is mentioned, no corresponding results appear in the Results section. Please either include this analysis in the Results or remove mention of the index from the Materials and Methods section.
3. d) For Non-metric Multi-Dimensional Scaling (MDS), you need to specify the similarity or dissimilarity index used and the type of data matrix (e.g., raw or transformed abundances, presence/absence). Although the Results section (line 223) mentions the use of Bray-Curtis similarity, MDS itself was not applied, and instead, a cluster analysis was performed. Ensure consistency by accurately describing the method used. If you opt to retain the cluster analysis, provide detailed information, including the clustering algorithm employed (e.g., single linkage, Ward’s, UPGMA), the similarity index used, and any constraints applied, if necessary.
4. e) The use of ANOSIM to test differences in community structure and composition between control and sand prawn treatments is appropriate. However, I do not follow the rationale for testing differences between groupings generated by the cluster analysis. Clusters that combine replicates from different treatments may not hold clear biological meaning. Please clarify the biological significance of these groupings or reconsider the relevance of this approach.

Response: Agree. I/We have, revised the statistical analysis, post hoc turkey test was conducted to ensure the reliability of the results. I/We re-wrote the entire section for statistical analysis (line 167 – 177), removed any mention of diversity as well as MDS.

NEW COMMENT 4:

Unfortunately, not all of my previous original comments (a–e) were adequately addressed.

a) The revised sentence is an improvement, but I suggest the following revision for greater clarity: “To test for differences between the mean values of the three treatments and the control in bioturbation rate, microphytobenthic algal concentration, macrofaunal abundance, and macrofaunal biomass, a one-way ANOVA followed by a post hoc Tukey test was employed.” However, please also consider my concerns in point b

b) You need to specify how the assumptions of ANOVA (i.e., normality and homoscedasticity) were tested to ensure the reliability of the results. Despite raising this issue in my initial review, the revised manuscript still does not provide this crucial information. This is particularly important, as an examination of the raw data in the Supplementary Material suggests that in many cases, either the normality test or the equal variance test may have failed. If these assumptions were not met, a parametric ANOVA would not be appropriate, and the non-parametric Kruskal–Wallis test should be used instead. This distinction is critical, as ANOVA compares mean values, whereas the Kruskal–Wallis test assesses differences in medians.

c–d) Thank you for removing references to Simpson’s diversity index and MDS analysis, as these were not used in the study.

e) Unfortunately, I must reiterate my previous concern: the rationale for testing differences between clusters using ANOSIM remains unclear. Furthermore, this approach is inconsistent with your statement in lines 173–176: "We used ANOSIM (Analysis of Similarities) to statistically test for significant differences in community composition among treatments. Similarity Percentage (SIMPER) analysis was then performed to determine which taxa contributed most to dissimilarities between treatments." In essence, while your goal is to assess differences in invertebrate community structures among treatments, the analysis as currently performed tests differences among clusters generated by UPGMA. More importantly, this approach is mathematically flawed. A fundamental principle of ANOSIM is that grouping must be predefined before analyzing the data. ANOSIM cannot be used to test differences between groups that were generated through cluster analysis or other post hoc data inspection, as this results in circular reasoning. Thus, the appropriate application of ANOSIM in your study would be a one-way ANOSIM to test the null hypothesis that there are no differences in community structure and composition among treatments. Given these concerns, I urge you to reconsider whether cluster analysis is truly necessary for your study and whether it should be included in the manuscript at all.

 

Original Comment 12: The section Results is poorly written and contains numerous errors and deficiencies. It lacks essential raw data, which prevents reviewers and prospective readers from independently interpreting the findings or evaluating the validity of the methods used. I strongly recommend that the authors provide tables containing raw data for bioturbation, algal concentration, and macrofaunal abundance and biomass for each replicate under all experimental treatments and control conditions. These tables could be included as supplementary material to avoid adding bulk to the main article. Additionally, it would be helpful to include species-level raw abundance data for both epifauna and infauna within each cage to better assess the dataset's completeness and robustness.

Response 12: Agree. The raw data has been supplied in the form of tables as supplementary materials as suggested, Page 16 &17.

NEW COMMENT 5:

Thank you for adding the supplementary materials. However, the numbering of the supplementary tables should follow the journal’s formatting requirements. It is unclear whether the first table in the Supplementary Material should be designated as Table 2. Additionally, some supplementary tables remain unnumbered (specifically, the last two, which present raw data for the caging experiments and macrofaunal species abundances in each treatment replicate). Please ensure that all supplementary tables are consistently numbered and properly cited within the main text—currently, only Table 5 is referenced. Furthermore, please use a period (.) as the decimal separator in the Supplementary Tables, and correct the typographical errors in the caption of the last table (“Macrofaunal species recorded during the experiment experiments conducted…”).

 

Original Comment 13: The statistical analysis results for bioturbation rates (lines 175–179) are inconsistent with what is depicted in Fig. 2a. In Fig. 2a, different letters ("a" to "d") denote statistically significant differences between each treatment and the control. However, the text states: “ANOVA indicated that the bioturbation rates in Treatments 2 and 3 were significantly higher than those recorded in the Control and Treatment 1 (F = 29.78; P < 0.001). There were no significant differences in the bioturbation rates between Treatment 2 and Treatment 3 (P > 0.05). Similarly, the bioturbation rates in the Control and Treatment 1 were not significantly different from one another (P > 0.05).” Please reconcile these discrepancies between the textual description and the figure. Furthermore, the textual results often redundantly restate information presented in figures, such as Fig. 2a. Instead, textual descriptions should complement figures by providing additional insights rather than repeating visual data. This suggestion applies throughout the Results section.

Response: Agree. I/We have modified and re-wrote this section to correct these inconsistencies (line 181 – 187).

NEW COMMENT 6:

There is still an inconsistency between the statistical results for bioturbation rates and the data presented in Figure 2a. In Figure 2a, different letters ("b" and "c") indicate statistically significant differences between Treatments 2 and 3. However, the text states (lines 186–187): “No significant differences were observed between Treatments 2 and Treatment 3 (P > 0.05)…” Please resolve this discrepancy between the figure and the textual description.

 

Original Comment 14: Similar inconsistencies appear in other subsections of the Results (5.1.2, 5.1.3, and 5.1.4) in relation to Fig. 2. For instance, lines 186–187 state: “ANOVA revealed that there was a significant difference between all treatment groups (F = 3.48; P < 0.05).” However, Fig. 2b shows Treatment 1 as “ab,” indicating no significant difference between the control and Treatment 1, or between Treatment 1 and Treatment 2. Given the high variability (SD) in the control, Treatments 2, and 3, significant differences in Chl-a concentration between these treatments seem unlikely. These inconsistencies undermine confidence in the results and must be addressed

Response: Agree. I/We have modified and re-wrote these results to address these conflicting statements, subsection 4.2 – 4.4 (line 189 – 207).

NEW COMMENT 7:

Additional remarks regarding Sections 4.2., 4.3. and 4.4.: a) Please add the F and P values from the ANOVA analysis in line 190. b) Specify what Treatment is being referred to in line 202. c) Clarify what the symbol “s” represents in line 204? d) The notation of the probability value in line 204 is incorrect (P=<0.001⁵), please correct it.

 

Original Comment 15: The whisker lengths in Fig. 2b for Treatment 1 do not correspond to the value provided in line 183 (SD = 0.61), which is almost equal to the treatment's mean value (0.627). Please correct this discrepancy.

Response: Agree. I/We have changed the SD to SE to show variability between sample means (lines 212).

NEW COMMENT 8:

The whisker lengths in Figure 2 still do not appear to correspond to the standard error (SE) values provided in the Supplementary Tables. For example, in the case of the bioturbation rate for the control, the SE is 0.003 (see Table 2), whereas the whisker length in Figure 2a appears to be nearly half the control mean value (~0.012). Please verify and correct any discrepancies between the figure and the reported SE values.

 

Original Comment 16: In subsections 5.1.3 and 5.1.4, macrofaunal abundance and biomass are reported as individuals m^-³ and mg wwt m^-³, respectively. This unit implies that only infauna was analyzed. What about epifauna (abundance of what should be expressed as ind m^-2)? Please clarify whether epifauna were excluded or provide appropriate units.

Response: Agree. I/We have, accordingly, done/revised/changed/modified to emphasize this point, biomass was reported as grams wet weight per square meter (g wwt/m²) to account for both infaunal and epifaunal organisms (Figure 2).

NEW COMMENT 9:

Contrary to what you state above in your Response, in Figure 2 macrobenthic abundance and biomass are expressed per cubic meter (m³), not per square meter (m²). For instance, in Figure 2a, the Y-axis label reads: “BIOTURBATION RATES g cm2 h¹”, but it should be formatted as “BIOTURBATION RATE g cm^-2 h^-1”. Please correct all Y axes titles in Figure 2. Please ensure uniform formatting, adhering to the journal's preferred style and using consistently throughout either solidus or negative exponent in symbols formed by division (compare e.g., line 57: “100 ind m^-2” with line 125: “36 ind/m²” or line 104: “< 15 mg dwt m-3” (no superscript). Additionally, in the Figure 2 caption: a) Define SE as standard error. b) Clarify that different letters indicate significant differences detected by the post hoc Tukey test (not ANOVA).

 

Original Comment 24: Subchapter “5.1.6 Bray-Curtis Cluster Analysis” (lines 223–244), now 4.5. Bray Curtis Cluster Analysis (lines 212-233).

1. b) Line 224: Seven clusters (including an outlier) are visible at a 70% similarity level, not just two groups as claimed. The two groups emerge at the 60% similarity level.
2. c) Line 226: Group 2 includes samples from the control and all three treatments, not just Treatments 2 and 3 as erroneously stated.
3. e) Cluster analysis may not be the best approach for this study. An MDS plot would better visualize overall variation in the multivariate dataset, while differences should be tested using a robust multivariate method such as ANOSIM or PERMANOVA between treatments rather than relying on cluster groupings.
4. h) Table 1: This table is not referenced in the text. Additionally, please format the table properly, including consistent decimal places and clearer species names (e.g., by wrapping text in cells).

Response: Agree. I/We have modified and re-wrote the entire Hierarchical cluster analysis section, removed MDS, changed figure caption and described the SIMPER analysis properly in methods (line 175 – 177 & 215 – 230.

NEW COMMENT 10:

The subsection 4.5. Bray Curtis Cluster Analysis still requires further revision. The following issues remain unaddressed.

Line 213: I can repeat again: At a 70% similarity level (represented as 0.7 in Figure 3), there are seven clusters (including an outlier), not just two groups as claimed. If you consider the two groups indicated by blue lines, these emerge at the 0.6 similarity level, not 0.7. Please correct this statement.

Line 215: Group 2 includes samples from the control and all three treatments, not just Treatments 2 and 3 as incorrectly stated.

Lines 216-217. As previously mentioned, cluster analysis may not be the most appropriate method for this study. However, if you choose to retain it as a way to visualize variation in your multivariate dataset, ANOSIM should be used to test differences between treatments, not between cluster groupings (see my previous comments).

Lines 222-226. SIMPER should be applied to determine the contribution of individual macroinvertebrate species to differences between treatments, not between clusters derived from the cluster analysis.

Table 1 should be referenced in the text when presenting the SIMPER analysis results (lines 222-226). Currently, Table 1 is first cited in the Discussion section. Also, please properly format the table, ensuring consistent decimal places and clearer species names (e.g., use text wrapping within cells for readibility).

 

NEW COMMENT 11:

The Discussion section (and likely the Conclusions and Abstract) will need revisions following the necessary corrections to the macroinvertebrate community analyses and the reinterpretations outlined in my previous comments.

 

Edits

Original comment: Numerous deficiencies require attention. Below are examples, but the entire manuscript should be carefully reviewed and edited.

Response 1: (The entire manuscript has been reviewed and hopefully fixed all the suggested edits (Page 1 to page 18).

NEW COMMENT 12:

Several formatting and editorial inconsistencies remain unaddressed. Below are some specific examples; however, the entire manuscript should be carefully re-edited to ensure consistency.

1) Headings: The formatting of section titles is still inconsistent. Compare the section: “1. Introduction” with section “2. STUDY SITES” written in uppercase, and with section “3.4. Statistical analysis” italicized. Please standardize these in accordance with journal guidelines.

 

2) Citations: Check for missing or incorrect references (e.g., reference no. 32 in line 404), and ensure again that references in the text follow ascending order (e.g., line 264).

3) Spacing: a) Maintain consistent spacing between numbers and units (e.g., compare “1m” with 100 ind m^-2” in line 57 or “1 cm” in line 154 with “0.1g” in line 166). b) Ensure proper spacing around mathematical symbols (e.g., correct "F= 21.37” in line 204 and similar instances in line 217). c) Several unnecessary double spaces between words remain in the text (e.g., in lines: 104, 108, 175, 203, 287, 289, 300).

4) Italicization of statistical symbols: Ensure uniform formatting of F and P values in ANOVA results (compare F in italics and P in plain text in line 182 with F in plain text in line 193 and P in italics in line 186). Maintain consistent italicization throughout.

5) Punctuation: a) Missing full stops in lines 24, 150 and 226. b) A misplaced full stop before a citation in line 30.

6) Typographical Errors: a) Line 86: Insert “in” between “role” and “nutrient”. b) Line 187 and 194: Correct "Treatments 2" to "Treatment 2”. c) Line 524: Correct “Suplimentary” to “Supplementary”.

7) Species names: Ensure species names are consistently italicized in titles of cited works in the reference list.

Response: All species name have been written in italics in the references and throughout the manuscript.

NEW COMMENT: Look at Upogebia africana in line 327.

Author Response

We sincerely appreciate the time and effort you have dedicated to reviewing our manuscript. Below, we provide detailed responses to each of your comments, with corresponding revisions clearly highlighted in red the resubmitted manuscript. Thank you again for your valuable feedback.

 

 

 

Original Comment 6: There appears to be no reference to Fig. 1 in this section. Please ensure this figure is appropriately cited where relevant.

 

Response: The figure was referenced after the caption (please see line 115, previously line 108].

 

NEW COMMENT 1:

 

There is still no explicit reference to Figure 1 within the "Study Site" section or elsewhere in the manuscript, as was also the case in the original submission. The only mention of this figure is in the caption (lines 115–116, previously lines 108–109), but it is not cited in the text. Please ensure that Figure 1 is appropriately referenced in the main text. Additionally, the citation in the figure caption, which refers to the source of the map (i.e., Froneman, 2013), should be formatted numerically rather than by author name and year.

Response: Thank you for your feedback. Figure 1 has now been explicitly cited in the Study Site section (lines 93 and 122). Additionally, the reference to Froneman (2013) has been replaced with a numerical citation [5] in line 115, ensuring consistency with the journal’s citation format.

Original Comment 7: For species names, it is standard practice to include taxonomic authorities upon their first mention. For instance, line 99 could be revised to Pseudodiaptomus hessei (Mrázek) and Paracartia longipatella (Connell & Grindley). If you agree with this convention, please apply it consistently throughout the manuscript.

 

Response: Agree and thank you for pointing this out. I/We have effected these changes accordingly throughout the manuscript, to emphasize this point. Taxonomic authorities for species have been included [line 105 – 109].

 

NEW COMMENT 2:

 

Thank you for adding taxonomic authorities; however, they should not be italicized, unlike species names. Please ensure that taxonomic authorities are presented in plain text. Additionally, species collected during the study still lack taxonomic authorities (see page 8, lines 224–225, as well as Table 1 and the final unnumbered table in the Supplementary Material), leading to inconsistency in the manuscript. I strongly recommend including taxonomic authorities for species names in both tables. This would eliminate the need to repeatedly provide taxonomic authorities for collected species throughout the text.

 

Response: Thank you for pointing this out. Taxonomic authorities have been corrected to plain text throughout the manuscript, including in Table 1 (line 223–224) and the Supplementary Material. This ensures consistency in formatting.

 

Original Comment 10: In Subchapter “3.1.3 Epifauna and infauna community structure” (lines 148–156), you describe the methods for assessing total abundance and biomass of epi- and infauna and the identification key used. However, it is unclear how the community structure was described and analyzed (e.g., what indices were employed). Please provide this missing information.

 

Response: Agree, and thank you for pointing this out I/We have, removed this section from the manuscript for further analysis.

 

NEW COMMENT 3:

 

The section now titled “3.3. Macrofaunal Community” remains in the revised manuscript. If you have not provided methods for analyzing community structure, I recommend modifying the phrase in line 161 from “The macrofaunal community structure…” to “The macrofaunal abundance, biomass, and community composition…” to align with the description in lines 140–141. Additionally, please clearly indicate (as done in subsections 3.1. and 3.2.) that macroinvertebrate abundance and biomass are expressed as the number of individuals per m³ and mg wet weight per m³, respectively.

 

Response: The phrase in line 160 has been modified to "macrofaunal abundance, biomass, and community composition" to align with line 140. The units of measurement for abundance and biomass (individuals per m³ and mg wet weight per m³) are now clearly stated (lines 164–165). To better reflect the analytical approach, the cluster analysis description (including the Bray-Curtis similarity index) has been moved from "Statistical Analysis" to "Macrobenthic Community" to improve logical flow.

 

 

However, I would argue that since cluster analysis and SIMPER were employed, you have, in fact, analyzed macrofaunal community structure. Moving the description of these methods—specifically, cluster analysis (which should explicitly mention the similarity index used, i.e., Bray–Curtis)—from subsection “3.4. Statistical Analysis” to section “3.3. Macrofaunal Community” would better reflect your approach. This restructuring would also improve logical flow, as cluster analysis and SIMPER are not strictly statistical methods. However, please also refer to my concerns in NEW COMMENT 4e.

Macrofauna was changed to macrobenthic community structure throughout the manuscript since it encompasses the overall ecological characteristics of macrofauna like abundance, biomass, distribution and composition.

Response: We appreciate your feedback and have corrected our statistical approach to align with best practices. ANOSIM is now conducted as a one-way analysis, testing for differences in community composition among predefined treatments, rather than clusters. The methods section has been revised to explicitly state that UPGMA clustering was exploratory and not used for statistical testing (lines 173–176). The interpretation of ANOSIM results in the Results and Discussion sections has been updated accordingly.

 

 

Original Comment 11: The chapter “4. Statistical analyses” (lines 157–165) lacks several crucial details: a) Specify what aspects you tested for significant differences between treatments using one-way ANOVA done. Were these differences evaluated in terms of a bioturbation rates, microphytobenthic algal concentration, epi- and infaunal abundance, and epi- and infaunal biomass?

 

1. b) Since ANOVA is a parametric method, it is essential to explain how you assessed whether its assumptions (normality and homoscedasticity) were met to ensure the reliability of results.
2. c) Although Simpson’s diversity index is mentioned, no corresponding results appear in the Results section. Please either include this analysis in the Results or remove mention of the index from the Materials and Methods section.
3. d) For Non-metric Multi-Dimensional Scaling (MDS), you need to specify the similarity or dissimilarity index used and the type of data matrix (e.g., raw or transformed abundances, presence/absence). Although the Results section (line 223) mentions the use of Bray-Curtis similarity, MDS itself was not applied, and instead, a cluster analysis was performed. Ensure consistency by accurately describing the method used. If you opt to retain the cluster analysis, provide detailed information, including the clustering algorithm employed (e.g., single linkage, Ward’s, UPGMA), the similarity index used, and any constraints applied, if necessary.
4. e) The use of ANOSIM to test differences in community structure and composition between control and sand prawn treatments is appropriate. However, I do not follow the rationale for testing differences between groupings generated by the cluster analysis. Clusters that combine replicates from different treatments may not hold clear biological meaning. Please clarify the biological significance of these groupings or reconsider the relevance of this approach.

Response: Agree. I/We have, revised the statistical analysis, post hoc turkey test was conducted to ensure the reliability of the results. I/We re-wrote the entire section for statistical analysis (line 167 – 177), removed any mention of diversity as well as MDS.

 

NEW COMMENT 4:

 

Unfortunately, not all of my previous original comments (a–e) were adequately addressed.

 

1. a) The revised sentence is an improvement, but I suggest the following revision for greater clarity: “To test for differences between the mean values of the three treatments and the control in bioturbation rate, microphytobenthic algal concentration, macrobenthic abundance, and biomass, a one-way ANOVA followed by a post hoc Tukey test was employed.” However, please also consider my concerns in point b

4a) The statement has been revised accordingly for better comprehension (section 3.4; line 169 – 171). Additionally, we used the Kruskal-Wallis test and Dunn`s post hoc test instead of the ANOVA like you suggested.

1. b) You need to specify how the assumptions of ANOVA (i.e., normality and homoscedasticity) were tested to ensure the reliability of the results. Despite raising this issue in my initial review, the revised manuscript still does not provide this crucial information. This is particularly important, as an examination of the raw data in the Supplementary Material suggests that in many cases, either the normality test or the equal variance test may have failed. If these assumptions were not met, a parametric ANOVA would not be appropriate, and the non-parametric Kruskal–Wallis test should be used instead. This distinction is critical, as ANOVA compares mean values, whereas the Kruskal–Wallis test assesses differences in medians.

I/We appreciate your detailed feedback and acknowledge the need to explicitly state how the assumptions of ANOVA (normality and homoscedasticity) were assessed to ensure the reliability of our statistical results. Additionally, since I have a small data set I decided to take your advice and use the Kruskal-Wallis test instead of the ANOVA.         

 

c–d) Thank you for removing references to Simpson’s diversity index and MDS analysis, as these were not used in the study.

 

1. e) Unfortunately, I must reiterate my previous concern: the rationale for testing differences between clusters using ANOSIM remains unclear. Furthermore, this approach is inconsistent with your statement in lines 173–176: "We used ANOSIM (Analysis of Similarities) to statistically test for significant differences in community composition among treatments. Similarity Percentage (SIMPER) analysis was then performed to determine which taxa contributed most to dissimilarities between treatments." In essence, while your goal is to assess differences in invertebrate community structures among treatments, the analysis as currently performed tests differences among clusters generated by UPGMA. More importantly, this approach is mathematically flawed. A fundamental principle of ANOSIM is that grouping must be predefined before analyzing the data. ANOSIM cannot be used to test differences between groups that were generated through cluster analysis or other post hoc data inspection, as this results in circular reasoning. Thus, the appropriate application of ANOSIM in your study would be a one-way ANOSIM to test the null hypothesis that there are no differences in community structure and composition among treatments. Given these concerns, I urge you to reconsider whether cluster analysis is truly necessary for your study and whether it should be included in the manuscript at all.

 

 Response: We have revised our statistical approach so that ANOSIM is now conducted as a one-way analysis, testing for differences in community composition among the predefined treatment groups (Control, Treatment 1, Treatment 2, Treatment 3), rather than among clusters. The description of our statistical methods has been updated to clarify that UPGMA clustering was performed as an exploratory tool to visualize similarities but was not used as the basis for statistical testing. We have carefully revised our interpretation of the results to ensure they align with the corrected analysis.

 

Original Comment 12: The section Results is poorly written and contains numerous errors and deficiencies. It lacks essential raw data, which prevents reviewers and prospective readers from independently interpreting the findings or evaluating the validity of the methods used. I strongly recommend that the authors provide tables containing raw data for bioturbation, algal concentration, and macrofaunal abundance and biomass for each replicate under all experimental treatments and control conditions. These tables could be included as supplementary material to avoid adding bulk to the main article. Additionally, it would be helpful to include species-level raw abundance data for both epifauna and infauna within each cage to better assess the dataset's completeness and robustness.

 

Response 12: Agree. The raw data has been supplied in the form of tables as supplementary materials as suggested, Page 16 &17.

 

NEW COMMENT 5:

 

Thank you for adding the supplementary materials. However, the numbering of the supplementary tables should follow the journal’s formatting requirements. It is unclear whether the first table in the Supplementary Material should be designated as Table 2. Additionally, some supplementary tables remain unnumbered (specifically, the last two, which present raw data for the caging experiments and macrofaunal species abundances in each treatment replicate). Please ensure that all supplementary tables are consistently numbered and properly cited within the main text—currently, only Table 5 is referenced. Furthermore, please use a period (.) as the decimal separator in the Supplementary Tables, and correct the typographical errors in the caption of the last table (“Macrofaunal species recorded during the experiment experiments conducted…”).

Response: Thank you for the comment, the numbering of tables in the supplementary materials has been revised in accordance with the journal`s requirements (Pages 15 – 17). Previously unnumbered tables have been numbered (Page 16- 17). Additionally, tables in the supplementary materials have been referenced in the text and a period was utilized as a decimal separator in all Supplementary tables (Page 15 – 17).  I/we have corrected the typographical error in the final table caption.

 

 

Original Comment 13: The statistical analysis results for bioturbation rates (lines 175–179) are inconsistent with what is depicted in Fig. 2a. In Fig. 2a, different letters ("a" to "d") denote statistically significant differences between each treatment and the control. However, the text states: “ANOVA indicated that the bioturbation rates in Treatments 2 and 3 were significantly higher than those recorded in the Control and Treatment 1 (F = 29.78; P < 0.001). There were no significant differences in the bioturbation rates between Treatment 2 and Treatment 3 (P > 0.05). Similarly, the bioturbation rates in the Control and Treatment 1 were not significantly different from one another (P > 0.05).” Please reconcile these discrepancies between the textual description and the figure. Furthermore, the textual results often redundantly restate information presented in figures, such as Fig. 2a. Instead, textual descriptions should complement figures by providing additional insights rather than repeating visual data. This suggestion applies throughout the Results section.

 

Response: Agree. I/We have modified and re-wrote this section to correct these inconsistencies (line 181 – 187).

 

NEW COMMENT 6:

 

There is still an inconsistency between the statistical results for bioturbation rates and the data presented in Figure 2a. In Figure 2a, different letters ("b" and "c") indicate statistically significant differences between Treatments 2 and 3. However, the text states (lines 186–187): “No significant differences were observed between Treatments 2 and Treatment 3 (P > 0.05)…” Please resolve this discrepancy between the figure and the textual description.

 

Response: Thank you for pointing out the inconsistency. We have reanalyzed the data using the Kruskal-Wallis test, as previously suggested. The entire results section has been updated accordingly in both the text (page 6) and Figure 2a to ensure consistency between statistical findings and graphical representation. The lettering in Figure 2a now accurately reflects the statistical differences indicated by Dunn’s post hoc test.

 

Original Comment 14: Similar inconsistencies appear in other subsections of the Results (5.1.2, 5.1.3, and 5.1.4) in relation to Fig. 2. For instance, lines 186–187 state: “ANOVA revealed that there was a significant difference between all treatment groups (F = 3.48; P < 0.05).” However, Fig. 2b shows Treatment 1 as “ab,” indicating no significant difference between the control and Treatment 1, or between Treatment 1 and Treatment 2. Given the high variability (SD) in the control, Treatments 2, and 3, significant differences in Chl-a concentration between these treatments seem unlikely. These inconsistencies undermine confidence in the results and must be addressed

 

Response: Agree. I/We have modified and re-wrote these results to address these conflicting statements, subsection 4.2 – 4.4 (line 189 – 207).

 

NEW COMMENT 7:

 

Additional remarks regarding Sections 4.2., 4.3. and 4.4.: a) Please add the F and P values from the ANOVA analysis in line 190. b) Specify what Treatment is being referred to in line 202. c) Clarify what the symbol “s” represents in line 204? d) The notation of the probability value in line 204 is incorrect (P=<0.0015), please correct it.

1. The new P Values have been included in the text
2. The treatment being referred to in line 203 has been specified.
3. The s in line 205 was a formatting error
4. Probability value notation in (line 205) has been revised accordingly.

 

 

 

Original Comment 15: The whisker lengths in Fig. 2b for Treatment 1 do not correspond to the value provided in line 183 (SD = 0.61), which is almost equal to the treatment's mean value (0.627). Please correct this discrepancy.

 

Response: Agree. I/We have changed the SD to SE to show variability between sample means (lines 212).

 

NEW COMMENT 8:

 

The whisker lengths in Figure 2 still do not appear to correspond to the standard error (SE) values provided in the Supplementary Tables. For example, in the case of the bioturbation rate for the control, the SE is 0.003 (see Table 2), whereas the whisker length in Figure 2a appears to be nearly half the control mean value (~0.012). Please verify and correct any discrepancies between the figure and the reported SE values.

 

Response: I/We have verified and corrected the whisker lengths in Figure 2 to ensure they accurately reflect SE values from Supplementary Tables. The figure now correctly represents variability, improving accuracy.

 

 

 

Original Comment 16: In subsections 5.1.3 and 5.1.4, macrofaunal abundance and biomass are reported as individuals m-³ and mg wwt m-³, respectively. This unit implies that only infauna was analyzed. What about epifauna (abundance of what should be expressed as ind m-2)? Please clarify whether epifauna were excluded or provide appropriate units.

 

Response: Agree. I/We have, accordingly, done/revised/changed/modified to emphasize this point, biomass was reported as grams wet weight per square meter (g wwt/m²) to account for both infaunal and epifaunal organisms (Figure 2).

 

NEW COMMENT 9:

 

Contrary to what you state above in your Response, in Figure 2 macrobenthic abundance and biomass are expressed per cubic meter (m3), not per square meter (m2). For instance, in Figure 2a, the Y-axis label reads: “BIOTURBATION RATES g cm2 h1”, but it should be formatted as “BIOTURBATION RATE g cm-2 h-1”. Please correct all Y axes titles in Figure 2. Please ensure uniform formatting, adhering to the journal's preferred style and using consistently throughout either solidus or negative exponent in symbols formed by division (compare e.g., line 57: “100 ind m-2” with line 125: “36 ind/m2” or line 104: “< 15 mg dwt m-3” (no superscript). Additionally, in the Figure 2 caption: a) Define SE as standard error. b) Clarify that different letters indicate significant differences detected by the post hoc Tukey test (not ANOVA).

We appreciate the reviewer’s careful attention to detail and have made the necessary corrections to ensure consistency and adherence to the Diversity journal’s preferred formatting style. Specifically:

Response: The Y-axis label in Figure 2a has been corrected from “BIOTURBATION RATES g cm2 h1” to “BIOTURBATION RATE (g cm⁻² h⁻¹) and similar corrections have been applied to all other Y-axis labels in Figure 2 to ensure uniform formatting. Macrobenthic abundance is now consistently expressed as ind m⁻³ throughout the manuscript and macrobenthic biomass is now consistently expressed as mg dwt m⁻³ and the previously inconsistent notations (e.g., 36 ind/m² and 100 ind m⁻³) have been revised to use the negative exponent format consistently.

SE has been defined as Standard error and b) it has been made clear that different letters indicate significant differences detected by the Dunn`s post hoc test not ANOVA as previously stated.

 

 

 

Original Comment 24: Subchapter “5.1.6 Bray-Curtis Cluster Analysis” (lines 223–244), now 4.5. Bray Curtis Cluster Analysis (lines 212-233).

 

1. b) Line 224: Seven clusters (including an outlier) are visible at a 70% similarity level, not just two groups as claimed. The two groups emerge at the 60% similarity level.
2. c) Line 226: Group 2 includes samples from the control and all three treatments, not just Treatments 2 and 3 as erroneously stated.
3. e) Cluster analysis may not be the best approach for this study. An MDS plot would better visualize overall variation in the multivariate dataset, while differences should be tested using a robust multivariate method such as ANOSIM or PERMANOVA between treatments rather than relying on cluster groupings.
4. h) Table 1: This table is not referenced in the text. Additionally, please format the table properly, including consistent decimal places and clearer species names (e.g., by wrapping text in cells).

Response: Agree. I/We have modified and re-wrote the entire Hierarchical cluster analysis section, removed MDS, changed figure caption and described the SIMPER analysis properly in methods (line 175 – 177 & 215 – 230.

 

NEW COMMENT 10:

 

The subsection 4.5. Bray Curtis Cluster Analysis still requires further revision. The following issues remain unaddressed.

 

Line 213: I can repeat again: At a 70% similarity level (represented as 0.7 in Figure 3), there are seven clusters (including an outlier), not just two groups as claimed. If you consider the two groups indicated by blue lines, these emerge at the 0.6 similarity level, not 0.7. Please correct this statement.

Response: This statement has been revised to show that the two major groups circled in blue emerged at 60 percent similarity and no 70 percent as stated before (Line 211).

 

Line 215: Group 2 includes samples from the control and all three treatments, not just Treatments 2 and 3 as incorrectly stated.

 

Response: Group 2 has been corrected to include all treatments, control and treatment 1 have been added to the statement (Line 213).

 

Lines 216-217. As previously mentioned, cluster analysis may not be the most appropriate method for this study. However, if you choose to retain it as a way to visualize variation in your multivariate dataset, ANOSIM should be used to test differences between treatments, not between cluster groupings (see my previous comments).

 

Response: Agreed, and thank you for not getting tired of repeating your comments. It has been clearly stated that ANOSIM was used to test for differences between treatments not the cluster groups (Line 175 & 214 - 215).

 

Lines 222-226. SIMPER should be applied to determine the contribution of individual macroinvertebrate species to differences between treatments, not between clusters derived from the cluster analysis.

 

Response: Thank you for your comment, SIMPER now shows that it was conducted to help determine which species contributed to the differences between treatments (Line 178, 221)

 

Table 1 should be referenced in the text when presenting the SIMPER analysis results (lines 222-226). Currently, Table 1 is first cited in the Discussion section. Also, please properly format the table, ensuring consistent decimal places and clearer species names (e.g., use text wrapping within cells for readibility).

 

Response: Table 1 has been cited in the results section and formatted accordingly with clear species names and consistent decimal places. page 8

 

NEW COMMENT 11:

 

The Discussion section (and likely the Conclusions and Abstract) will need revisions following the necessary corrections to the macroinvertebrate community analyses and the reinterpretations outlined in my previous comments.

 

 

 

Edits

 

Original comment: Numerous deficiencies require attention. Below are examples, but the entire manuscript should be carefully reviewed and edited.

 

Response 1: (The entire manuscript has been reviewed and hopefully fixed all the suggested edits (Page 1 to page 18).

 

NEW COMMENT 12:

 

Several formatting and editorial inconsistencies remain unaddressed. Below are some specific examples; however, the entire manuscript should be carefully re-edited to ensure consistency.

 

• Headings: The formatting of section titles is still inconsistent. Compare the section: “1. Introduction” with section “2. STUDY SITES” written in uppercase, and with section “3.4. Statistical analysis” italicized. Please standardize these in accordance with journal guidelines.

Headings have been fixed, STUDY CITES edited to be Study sites and Statistical analysis is no longer Italicized.

 

 

 

• Citations: Check for missing or incorrect references (e.g., reference no. 32 in line 404), and ensure again that references in the text follow ascending order (e.g., line 264).

 

Response: 1. Headings have been standardized to follow journal guidelines.

2. Citations are now in ascending order (e.g., line 264).

 

• Spacing: a) Maintain consistent spacing between numbers and units (e.g., compare “1m” with 100 ind m-2” in line 57 or “1 cm” in line 154 with “0.1g” in line 166). b) Ensure proper spacing around mathematical symbols (e.g., correct "F= 21.37” in line 204 and similar instances in line 217). c) Several unnecessary double spaces between words remain in the text (e.g., in lines: 104, 108, 175, 203, 287, 289, 300).

Response: Thank you for your detailed feedback. We have carefully reviewed the manuscript and made the following corrections to ensure consistency and accuracy in formatting:

1. a) Spacing between numbers and units has been standardized (e.g., "1m" was corrected to "1 m" and "0.1g" to "0.1 g").
2. b) Proper spacing around mathematical symbols has been applied (e.g., "F= 21.37" was corrected to "F = 21.37").
3. c) Unnecessary double spaces between words have been removed throughout the manuscript, including the specific instances noted (lines 104, 108, 175, 203, 287, 289, and 300).

 

4) Italicization of statistical symbols: Ensure uniform formatting of F and P values in ANOVA results (compare F in italics and P in plain text in line 182 with F in plain text in line 193 and P in italics in line 186). Maintain consistent italicization throughout.

 

5) Punctuation: a) Missing full stops in lines 24, 150 and 226. b) A misplaced full stop before a citation in line 30.

 

6) Typographical Errors: a) Line 86: Insert “in” between “role” and “nutrient”. b) Line 187 and 194: Correct "Treatments 2" to "Treatment 2”. c) Line 524: Correct “Suplimentary” to “Supplementary”.

Response: Suplimentary has been changed to Supplementary (Page 15).

 

 

7) Species names: Ensure species names are consistently italicized in titles of cited works in the reference list.

 

Response: All species name have been written in italics in the references and throughout the manuscript.

 

NEW COMMENT: Look at Upogebia africana in line 327.

Upogebia Africana has been italicized. line 336

Author Response File: Author Response.docx