Dear Dr. Lins,
I have read the answers that you have provided to the comments of both reviewers. I encourage you to submit a revised version of your work that takes into account the modifications mentioned in your answers. I would recommend that you try to deepen your answer to the comment n° 4 of Reviewer 2 who is concerned with the number of samples on which your study is based. He/she would like that you justify that this number is adequate to derive your conclusions. I would also recommend that you state very clearly by a few sentences (e.g. in the Introduction) what is the new findings that your study brings concerning the general understanding of the (environmental) processes that shape deep sea benthic biodiversity distribution.
This revised version will be then sent to both reviewers for approval.

Many thanks in advance for your efforts,
Kind regards
Marilaure Grégoire

Dear Dr. Lins,
I have received an evaluation of the revised version of your work. The reviewer is asking further revisions that need to be tackled. In particular, he is asking that throughout the manuscript you better specify the diversity that you are addressing and that you further clarify what you mean by different « scales ». He is also suggesting further analyses for explaining the differences in diversity in terms of variability of the environment.
Please consider all the comments before submitting a revised version of your work.
Kind regards
Marilaure Grégoire

Dear Dr. Lins,
I have reviewed the revised version of your manuscript, " Evaluating environmental drivers of spatial variability in free-living nematode assemblages along the Portuguese margin” and your response to the comments of the reviewer. I have found that concerns raised by the reviewer have been adequately addressed. Based on that I suggest that your manuscript be accepted for publications in Biogeosciences provided that you take into account the minor comments which are at the end of this letter.

Thank you for submitting your manuscript to Biogeosciences.

With kind regards
Marilaure Grégoire

Comments:
(The references have been taken from the annotated version)
Abstract, line 23: please briefly clarify what is meant by « spatial factors »
Line 29 “was” and not “were”
Line 32:is it really “environmental shifts” that you want to refer to or is it “difference in environmental variability”. Shift means abrupt changes.
Page 2: line 34: are 100-1000 m2 large spatial scales?
Page 5, lines 26-28: The different levels of diversity (beta1, beta2 and beta3) have already been defined above. There is no need to repeat their definition here.
Page 7, line 39: please use only J’ since evenness has already been defined above (it has to be done throughout the manuscript).
Page 8, line 29: J’ and not J
Page 8, Line 30 same remark above: Evenness has already been defined.
Page 9, line 39: contribute and not contributes
Page 10, line 1: please specify which beta diversity you are talking about (as defined above)
Page 11, line 1 SED has already been defined above same remark for DistLM
Conclusions: The conclusion has to be a synthesis of the main messages of your work. I find surprising that you analyze again figure 9 there. I would prefer that in the conclusions you mention the outcome of the analysis of Figure 9 but that you do not describe it (it can be done in the results).

Throughout the manuscript I am a little but confused because in some part you use beta1, beta2 and beta3 (that are defined in the Material and methods) while in some parts you speak about “beta diversity between transects, or between stations.) It would be clearer that you defined these different levels of diversity once and then you use the same denomination for referring to them throughout the manuscript.

Table 1: Please reformulate: For instance: Sampling details: Station name (“St” refers to shallow water station while “deep” refers to deep sea station), date of sampling, water depth (m), latitude and longitude. Three and four independent replicates have been taken respectively at the shallow and deep stations (see Materials and methods for details).

Figure 1: Please reformulate: Location of the stations sampled during the RV Belgica cruises (B2013/17: 10.06.2013-18…B2014/15:02.06.2014) Please use bathymetry rather than elevation (source?), This is not clear to me why the two figures on page 26 and 27 can not be combined into one single figure.

Figure 9, legend line 13: I am wondering why you use “assume”, I guess that you test which environmental variables are correlated. What do you mean by local/regional diversity? Remove the last line this is already said at the second line.

Dear Dr. Lins,

I have read the final revisions of your work and I am pleased to accept your manuscript for publication in Biogeosciences.

Thank you for having chosen Biogeosciences for publication of your work.

Kind regards,

Marilaure Grégoire