Comments to the Author:

Both referees acknowledge the potential relevance of this study, but they also raise a number of concerns, which must prevent us from offering to publish the paper in its present form. As reported by reviewer 1: objectives, experimental design, methods, results and discussion are not presented in a clear concise and well-structured way. So, it is really difficult to understand what authors have exactly done, and what they obtained

We therefore invite you to send a revised manuscript, in which you cleared up the writing and interpretation of the data. Then, it will be sent again for per-revision, and after that we can reach a decision regarding publication (based on revision reports). Please carefully considered all issues raised by the reviewer 1.

Dear Dra Williams et al

From two original reviewers, one of them suggested some additional changes, mainly focused on editing issues during introduction, M&M, results and discussion sections that could help to improve the overall quality of the manuscript (See below).

I invite you to resubmit your manuscript after addressing all these comments.


Reviewer 1 comments:

The article titled Microbial biobanking cyanobacteria-rich topsoil facilitates mine rehabilitation, by Wendy Williams and collaborators, is a resubmission of a previous manuscript that I reviewed some time ago. As I said in my previous review, this article explores a very important topic in ecological restoration: the rehabilitation of degraded soils provoked by mining activities. It has been a pleasure for me to read the new version, and to realize that authors have done a great job during these days to unequivocally improve the quality of the text. In its current version, the article is easy to follow and, perhaps much more important, the hypotheses and goals are clearly exposed. Methods are correctly applied. Results are robust and clear. And the discussion section presents a general view of the results within a framework of the current knowledge of the topic. Although I have some minor comments (please, see below), I think that the article is now ready to be published. The literature on this topic will beneficiate with the discoveries by Williams and collaborators. In any case, please, have a general look and rewrite some sentences and paragraphs. And highlight a little bit more in the discussion section the main discoveries of the work, for example, the discovery of some cyanobacteria genera that were previously not considered to be as pioneers of biological soil crust establishment.

SPECIFIC COMMENTS (by section)
ABSTRACT
In line 10, page 1, please, remove “removal” or “disturbance” to facilitate reading. Choose only one word.
In line 14, page 1, please, add a comma after “At J-A”.

INTRODUCTION
I think that the first sentence should be “Soil disturbance results in a loss of resources and often has long lasting effects on soil stability, nutrient cycling and surface hydrology in drylands (…)”.
In line 5, page 2, instead of “that”, use “the”.
In lines 6-7, page 2, I think that the sentence “…whereby…events” is not necessary.
The sentence of lines 9-10, page 2, should be moved to the next paragraph.
The first time you introduce the term “biological soil crust”, use “biological soil crust”, not “biocrust”.
I line 14, page 2, please remove “…from rainfall…”.
Please, read carefully the third paragraph of this section. It looks like to me a little bit repetitive.
In fact, and although the introduction is well-written and easy to follow, I would recommend the authors to include five main points, with this order:
1. The problem of mine activities on soil degradation in drylands,
2. Potential solutions to this problem by using biological soil crust natural activities,
3. Properties and services provided by biological soil crusts in drylands,
4. Recommendations to use biocrusts for soil rehabilitation after mine activities, and
5. Goals and hypotheses of the present work.
In general, the introduction has this scheme, but I think that the paper will improve a lot if authors follow my recommendations.
In line 26, page 3, please include a comma after “study”.

METHODS
In line 6, after Figure S1, I think that you should include “www.” before the URL information of the web site.
In general, you should clearly expose all along the methods section whether you measured your variables in the field or in the lab. For example, it is not clear for me if you used the penetrometer in the field or in the lab. This will facilitate comparison of results in the future.
In lines 9-10, page 7, I think that the sentence needs to be rewritten because it is difficult to understand in its current form.
Although statistical analyses are presented all along the methods section, I think that it is a better option to include a subsection in the section called “Data analyses” that includes all what authors have done with statistics. And authors should expose the statistical significance that they chose (0.1, 0.05, 0.01).

RESULTS
In line 14, page 9, “2YO” means 2 years old I suppose, but it is necessary to specify, mainly for non-native English speakers, like me.
In lines 1-10, page 10, authors present some very interesting discoveries that should highlight a little bit more. For example, in the discussion section, authors should mention them again and say that they are important because, until now, other cyanobacteria species were considered to be the pioneers in biocrust formation, but not the cyanobacteria that they saw in this work.
In line 3, page 10, add a comma, please, after “In this study”.
The second paragraph in page 10 is hard to follow. Please, rewrite.
Authors mention in page 10 that Symplocastrum and Symploca were codominant in the 2YO stockpile, but later in the discussion section they do not provide any potential explanation. And this is also a very interesting result to discuss in terms of ecological succession of cyanobacteria in biocrusts. Please, consider reviewing the literature and provide an explanation.
In lines 10-11, page 11, I suppose that you calculated richness, evenness and diversity with the Primer package, but it is not clear at all. This is why, in my opinion, it is important to have a subsection called “Data analyses” in the methods section.

DISCUSSION
In line 7, page 13, please add a comma after “In general”.
In the second paragraph in page 13, I see some contradictory ideas. Please, rewrite the whole paragraph.
The article by García-Pichel and Wojciechowski (2009) centers in the role of Microcoleus. And authors have not found a lot of Microcoleus in their work. So, please, use the cite with caution. In any case, as I said before, authors found other cyanobacteria that play a similar role to this of Microcoleus in North America. And they should highlight it, talking about biogeography, for example, or differences in biological crust formation and temporal succession. This is only an idea.
In line 30, page 14, please add a comma after “In China”.

CONCLUSIONS
I have no comments.

TABLES & FIGURES
Because authors have a lot of tables and figures, I deeply recommend including some of them as supplementary material. Please, include in the main text only figures and tables that support your main discoveries.

Dear Wendy et al
After the third revision of your work I found that you successfully solved most of the problem pointed by the reviewers, however still some few things that needs to be solved in order to improve overall quality of the paper.
As pointed by reviewer 1 during the last revision process, the indirection has been improved when compared with the previous version, but I still quite repetitive.
1. I think that you can improve it by following the structure suggested by the reviewer:
a. The problem of mine activities on soil degradation in drylands,
b. Potential solutions to this problem by using biological soil crust natural activities,
c. Properties and services provided by biological soil crusts in drylands,
d. Recommendations to use biocrusts for soil rehabilitation after mine activities, and
e. Goals and hypotheses of the present work.

2. Was Fluorescence measured on the Petri dishes or in the field ?

3. In section 2.3.1 you described 12 replicates per site, but you have only 8 samples, please clarify

4. Section 3.1 is called Eco-physiological properties of biocrust cyanobacteria. I wonder if Ph, E.C, etc are eco-physiological properties of biocrusts

5.. Significant differences between soil tipes/ land units/etc should be included in ALL different figures and tables, this can be easily done by using superscripts letters

6. I agree with reviewer comment, too many figures are included within the main document, are is it possible to remove some of them from the main text?
7. Figure comments:
Fig 1 and 2 can be easily combined in one , same for figure 4 and 5
Fig 6, 7 can be a and b part of the same figure
In fig 8, scale values from axes is missing
Figure 9 has not been referenced in the text, please move it to the supplement
Figure 10: Is it possible to use different colors for the different species or genera instead of different levels of green?
Fig 11: Does it represent different soils units of SMU. Please be consistent with definition and nomenclature
Figures and tables format should be homogenized

Moreover, figure citation order should be revised

Finally I would suggest reformatting some of the main conclusions, as some lines are general statements and not conclusions based on your results

Dear Wendy et al

After another revission of your manuscript I found that some points can be improved. My main concern is about the structure of the introduction and conclusions sections. Statisticall analisis and how them are shown can also be improved.

E.g: In a previous revision one of the reviewer suggested to modify the introduction as:

a. The problem of mine activities on soil degradation in drylands,
b. Potential solutions to this problem by using biological soil crust natural activities,
c. Properties and services provided by biological soil crusts in drylands,
d. Recommendations to use biocrusts for soil rehabilitation after mine activities, and
e. Goals and hypotheses of the present work.

but I still found some discrepancies in the current version which is structured in 5 main paragraphs as follow:
Cyanobacteria description
Disturbacne effect on soils (emphasis on cyanobacteria)
Effect of disturbance on cyanobacteria, specific example of mining, restoration with specific descrition of cyanobacteria
Mine rehabilitation, importance of cyanobacteria for active restoration
Biobanking

I have the feeling that the manuscript could be improved by modifying this section as previously suggested by the reviewer

Moreover, soil and biocrust type are not considered together in the analysis. Do there is a reason why soil and crust type is not included within the PERMANOVA?. to my point of view by doing this one can easily analyze importance of both factors and differences between both soil type and biocrust type in cyanobacteria composition

Please carefully check all comments within the pdf

After a carefully revision of the document I found it has improved from previous version. However I still found some issues that should be improved and will lead the paper easier to follow. They are mainly related to the way text is presented and required some text polishing.

INTRODUCTION
I suggested to work a little bite more on the introduction as it is still not fully connected.

M&M
Was microscopy done based on same samples used for physicochemical analisys?
not clear in the text

RESULTS
Check how significant differences are presented in tables and figures
Figure 8 still not clear, what are you comparing. Moreover, all treatments should include letters
Caption should be something like:
What mean age on undisturbed samples means?

Based on figure, section 3.4 still confusing for an external reader, I would like to see a clearer version with a well define story line


DISCUSSION
I also suggest to change first subsection to include the link between cyanobacterial community structure, nutrient cycling and soil stabilization, as this last part is missing within the discussion

Conclusions
I also recommended to rewrote in order to ask main objectives presented:
A general conclusion based on your main objective "to determine whether shallow biobanks of cyanobacterial-enriched topsoil would facilitate the recovery of essential soil microprocesses when re-spread following mine disturbance"

and 2 specific conclusion based on specific objectives:

1) Define the cyanobacterial community structure with a special focus on species that drive early colonization, nutrient cycling and soil stabilization
2) to examine the effects of stockpiling topsoil on cyanobacterial resilience to crushing and burial and their recovery following spreading of topsoil back across mined land.

Please revise changes proposed in the attached pdf and replace figure 8 for the definitive figure including significant differences between sampling depths