Introducing Base - the Biomes of Australian Soil Environments soil microbial diversity database By Bissett et al. Wonderful initiative, well written manuscript. Accept with modifications.

Main points

• The one thing I am most disappointed by is the practice of combining all samples from one sampling location into one replicate. If I understood this well, this severely limits the ecological relevance of the Base. This problem is obviously not solved by the pseudoreplication that is done by extracting the same sample three times (L 205, L 165), and so we can question whether the Base dataset is good enough to conduct large scale integration (as claimed in L 162). Please clarify and if needed discuss.
• Is there a policy of expanding the dataset in the future? For example, it is pointed out that all data is generated by single laboratories (but see below); does that exclude other labs from depositing their data?
• Quality of Fig. 3 is low, and I could not distinguish the text even on the downloaded Fig.
• Fig 4 is similar, but also has a poor layout and repeats Fig. 1.
• Table two: remove empty lines in table, add % classified for all categories of organisms and explain abbreviations

Minor comments:

• Table 1: "grain size" should be replaced with "particle size distribution" or "clay, silt, and sand content". "Position in the landscape" used in the text and table needs some explanation. The abbreviation "Exc" should be explained (probably replace with "extr").  Fig. 1: The arrow in Fig. can be thicker, so it is easier to see.
• The inclusion of the Australian Antarctic Territories (Davis Station - Fig. 1B) in Australian is contested. A note could be included stating that this claim is recognized by only four countries in the world (according to Wiki)
• Although it is the choice of the authors to make the Figs in this manuscript, it would have liked to see a map with more information (Fig. 1), for example the various biomes or vegetation types (as in Fig. 4 I think although the quality is too low to know). Or perhaps a precipitation/climate map.
• L 150: what is "IBRA 7" (reference, website, version 7)?
• L 153: remove "also"  Throughout the text: inconsistent use of commas
• L 177: inconsistent: "soil chemical and physical attributes were usually…" (this line), "single facilities were used …" (L 170), and L 313 ("by a single laboratory")
• L 188: insert "extractable" between "(DTPA)" and "trace"
•  L 197: add "distribution" after "soil particle size".
• L 228: unclear sentence starting with "after merging" … "sequences were merged". What was the reason to do that? What was the conclusion from this activity?
• L 285: should this be "6" representatives instead of "4" (see line 261)?
•  L 278: replace "ref" with appropriate reference.
•  L 309 and 316: If "EMP" is not used as an abbreviation, it can be removed
• L 322: insert "that" between "ensure" and "raw"
• L 357L abbreviation "BASE"!. Use "BASE" as this is the abbreviation introduced earlier.
• L 408. The "term community turnover" is surprising, as only one sample at one time is taken. Please elaborate wither the turnover is a research goal for the future or can be done today (as stated).
• L 417 and following: too many "Current"s
• presence of a summary at the end of the paper while there is an abstract seems strange.
• L 616: replace "positions" with "sites" or "locations"

Level of interest

Please indicate how interesting you found the manuscript:
An article of importance in its field

Quality of written English

Please indicate the quality of language in the manuscript:
Acceptable

Declaration of competing interests

Please complete a declaration of competing interests, considering the following questions:

1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of this
manuscript, either now or in the future?

2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?

3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?

4. Have you received reimbursements, fees, funding, or salary from an organization that
holds or has applied for patents relating to the content of the manuscript?

5. Do you have any other financial competing interests?

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If you can answer no to all of the above, write 'I declare that I have no competing interests'
below. If your reply is yes to any, please give details below.

I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named report
including any attachments I upload will be posted on the website along with the authors'
responses. I agree for my report to be made available under an Open Access Creative Commons
CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments
which I do not wish to be included in my named report can be included as confidential comments
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I agree to the open peer review policy of the journal.

Authors' response to reviews: (http://www.gigasciencejournal.com/imedia/3786814462011801_comment.pdf)

The paper is acceptable in its present form assuming the quality of the Figs can be improved as suggested.

Level of interest

Please indicate how interesting you found the manuscript:
An article of importance in its field

Quality of written English

Please indicate the quality of language in the manuscript:
Acceptable

Declaration of competing interests

Please complete a declaration of competing interests, considering the following questions:

1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of this
manuscript, either now or in the future?

2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?

3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?

4. Have you received reimbursements, fees, funding, or salary from an organization that
holds or has applied for patents relating to the content of the manuscript?

5. Do you have any other financial competing interests?

6. Do you have any non-financial competing interests in relation to this paper?

If you can answer no to all of the above, write 'I declare that I have no competing interests'
below. If your reply is yes to any, please give details below.

I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named report
including any attachments I upload will be posted on the website along with the authors'
responses. I agree for my report to be made available under an Open Access Creative Commons
CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments
which I do not wish to be included in my named report can be included as confidential comments
to the editors, which will not be published.

I agree to the open peer review policy of the journal.