Dear Dr Bischoff,

Many thanks for your responses to referee reports.

I agree with both referees that the confounding effect of soil moisture is significant, and has to be highlighted more from the beginning. All of the hypotheses are framed in terms of salinity/sodicity, but the concurrent gradient of moisture provides an alternative or additional explanatory factor. I’m not sure if a possible inclusion of actual soil water content could have resolved this, as the direct correlation will not allow you to separate the two impacts statistically. As suggested by the referees, and also accepted in your response, this moisture gradient has to be clarified early on and discussed appropriately. I would like to see a mention of this also in the abstract, as it will form an important aspect of the interpretation and ultimately the impact of your paper.

Adding a fourth hypothesis seems logical, as you so far lack a rationale for the microbial/PLFA analysis. This has to be motivated in the introduction, though ad it would be good if you can do this without adding much to the length of the manuscript.

Overall, I think that the rate of true replication and confounding impacts of salinity/sodicity with soil moisture limit your ability to draw firm conclusions. You do however present an impressive set of data, covering a wide range of angles for these systems. Given that the gradient in moisture and salinity are likely to coincide in many locations, you will have to make this a much stronger point in the revised manuscript. I am hopeful that your proposed revisions will result in a publishable manuscript, but will seek the views of the reviewers again before making a final decision.

I think the exercise overseen by Prof. Schmidt to discuss your manuscript as part of the 2nd year Asters training is great, and you received a lot of comments regarding clarity of methods and results. Incorporating the changes you indicate will help this manuscript to be accessible by a wider readership (including students at Masters level).

Some streamlining in the results section is advisable, as pointed our by referee 1. Please concentrate on results pertinent to your testing of hypotheses, and move additional, more descriptive information to supplemental presentations (such as soil mineralogy, as suggested).

The conclusions could be more succinct. Rather than providing a complete summary of all your findings, please focus on key results and avoid repeating methods/hypotheses too much. So a shorter assessment of the impact of findings, and outlook with regards to implications of your study would be good, resulting in an overall reduction in length of the concluding section.

There are a few detailed comments (clarity/language), which you are likely to pick up during revision and I won’t list here. One point however, in line 9/10: This is not clear – “along the salinity gradient” does not indicate whether you mean with increasing or decreasing salinity. Please rephrase.

Dear Dr Bischoff,

Many thanks for your revision on the manuscript. This has now been seen by one of the original referees, and they found your changes to be generally thorough, with a recommendation to publish after minor revisions. Please see the remaining comments by the referee, which I agree with entirely.
I think that the manuscript already reads well, and that the comments by the referee should support points you make, so should strengthen it. I concur that the first two paragraphs need some more attention to avoid repetition of detail and inclusion of soil types not addressed by your study (Solonetz). To maybe clarify, the comment regarding “PLFA from unspecific bacteria”, this should more accurately refer to “nonspecific PLFAs”.
I therefore encourage you to implement these remaining minor edits, so that we can move to final acceptance following a quick editorial review.

Best regards,
Jens-Arne Subke

Dear Dr Bischoff,

Many thanks for the revisions on the manuscript, which now reads very well. I contacted the referee who suggested the additional statement regarding water permeability of fungal vs. bacterial tissues to request a suitable citation, and they suggest that you cite: Lennon et al. (2012), Mapping the niche space of soil microorganisms using taxonomy and traits. Ecology, 93 (8) 1867-1879.

Regarding the use of “Gram+” and “Gram-“ for gram-positive and gram-negative bacteria, I agree with the referee that the shorthand is not helpful. As you only use the terms in a few places throughout the manuscript, there is no great benefit on the truncated term, and I would request that you change this to “gram positive (or negative) bacteria” throughout the text.

I hope that you can amend the manuscript quite easily to this effect, and look forward to receiving the final version for final approval.

Best regards,
Jens-Arne Subke