Dear Raffaella Casotti

Thanks for the comment. The analysis of autotrophic prokaryotes, the Cyanobacteria, was performed in conjunction with the phytoplankton counting using the classic Utermöhl sedimentation technique. We recognize that a significant fraction of benthic cyanobacteria and some other parameters were not measured, as they would require different methods and expertise. Thank you for taking the time to read our manuscript.

Sincerely yours,

Dear Dr. Carstensen,

Thank you for the valuable comments that will contribute to better align our data paper with the focus of ESSD. Your comments are in italics followed by our responses:

1- “datasets VI and VII appear to arise from exactly the same sampling program, even the associated environmental variables are exactly the same. If so, much of the information provided is redundant and it would be more logical to combine the two datasets into one single that includes both shrimps and fish assemblages. It is important to know, if the two data sets are actually subsets of the same sampling scheme, as this can have effect on how a combined dataset will be analysed”

Your interpretation is correct. Dataset VI is a subset of the same sampling scheme of dataset VII and presents similar environmental variables as sampling efforts were carried out together to optimize our limited logistical and financial resources. Biological samples processing, identification and data analysis were performed by two different research groups, hence originating two distinct datasets that share the same environmental variables. We have included the following text (line 309): “The datasets VI and VII are subsets of the same sampling scheme and the associated environmental variables are the same”. The publication as two distinct datasets is justified considering the possibility of users to search dataset VI or VII separately in the GBIF platform depending on their taxonomic interest. Although the PLEA datasets are presented together in this data paper, in the repository they can be found as individual datasets. Publishing separate datasets in the repository further contributes to them being findable and mainly, reusable (FAIR principles).

2-“ the abbreviation PLEA is introduced in the beginning but not always consistently employed throughout the manuscript. Please check the nomenclature for consistency”

The use of the abbreviation PLEA (Patos Lagoon Estuary and Adjacent marine coast) throughout the manuscript has been corrected as suggested in the revised manuscript.

3- comments/editorial suggestions of technical nature

Your editorial suggestions of a technical nature have been accepted.

4-“Line 184: If the sample for DSi was frozen then the authors should verify that this does not affect the sample. Problems with polymerization have been reported numerous times”,

In fact, it would be ideal to have freeze the filters were the samples were concentrated, instead of frozen samples. However, if samples are frozen for a short time, no modifications in the Chlorophyll structure are observed. 

Thank you for your time during this review process.

Sincerely yours,

Dear Referee #2,

Thank you for the comments. We recognize the importance of the missing parameters addressed in your comment. In fact, since the beginning of LTER-PLEA we have planned for the inclusion of heterotrophic prokaryotes in the sampling protocol but we never managed to have the necessary expertise in our group. Contaminants are another relevant set of variables for urbanized aquatic ecosystems that we wish we could monitor within the PLEA. Despite the relevance of these and other parameters, constant funding cuts have prevented us from expanding the set of Biological groups and environmental parameters analyzed. We have included the following text in the Potential use and Conclusions (line 733): "Despite the wide range of variables monitored, we acknowledge that several components that are key to assess ecosystem quality are missing from our dataset. We have plans to monitor contaminants and heterotrophic prokaryotes in the near future". Thank you for your time during this review process.

Sincerely yours,