Reviewer name and names of any other individual's who aided in reviewer	Petr Baldrian
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published papers. (If no, please inform the editor that you cannot review this manuscript.)	Yes
Is the language of sufficient quality?	No
Please add additional comments on language quality to clarify if needed
Are all data available and do they match the descriptions in the paper?	No
Additional Comments	I was not able to locate the items listed as references (26) and (27). Due to this, I was not able to fully evaluate the paper.
Are the data and metadata consistent with relevant minimum information or reporting standards? See GigaDB checklists for examples <a href="http://gigadb.org/site/guide" target="_blank">http://gigadb.org/site/guide</a>	No
Additional Comments	I was not able to locate the data, see above.
Is the data acquisition clear, complete and methodologically sound?	No
Additional Comments	More details on sampling (mode of sampling, area sampled, depth sampled, sample size, sample handling) is missing. Information on number of repetitive extractions of DNA and the size of sample for extraction is missing. Protocols of amplification and barcoding are referenced as (27), but I was not able to locate this reference. These details have to be provided in the text for both types of sequencers.
Is there sufficient detail in the methods and data-processing steps to allow reproduction?	Yes
Additional Comments	For fungal ITS, the ITS region should be extracted before annotation.
Is there sufficient data validation and statistical analyses of data quality?	No
Additional Comments	The authors do not report how do they deal with sequences of fungi that produce amplicons longer than 350 bases that can not be pair-end joint in the 2x200 base runs. Even the MiSeq 2x250 runs miss some fungal taxa (though not very many) and here the situation is still worse. For the length distribution of fungal ITS, please consult the UNITE database.
Is the validation suitable for this type of data?	No
Additional Comments	There should be additional validations including the analysis of those OTUs that are abundant in one setup but missing in another one (if any).
Is there sufficient information for others to reuse this dataset or integrate it with other data?	No
Additional Comments	The metadata, supossedly in reference (26) are impossible to locate.
Any Additional Overall Comments to the Author	I believe that this is a very good attempt to test the novel platform with fungal metabarcoding. If all required information is provided, I believe that this can be both an interesting paper and a valuable dataset.
Recommendation	Reject (Unsound or Unusuable)