Dear Anonymous Reviewer 1, first of all thank you for your torough revision, which will allow us to provide a more accurate description of the assemblage and trophic structure of the mesozooplanktonic communities of the Adriatic basi, please find below a poit-by-poit replies to your concerns, while we’re preparing an edited version of the manuscript, once received  apoisitve reply from the editor.

Best regards Emnauela Fanelli

AR1

This manuscript provides a description of the differences in taxonomic composition and several trophic indicators of mesozooplankton between several subregions. The authors claim that this is the first study covering both shallow and deep waters across the whole Adriatic basin, a productive ecosystem within the otherwise oligotrophic Mediterranean sea. From plankton data collected in a single cruise, several communities were characterized from abundance and biomass composition assemblages as well as by their values of natural abundance of stable carbon and nitrogen isotopes.  While the description of the characteristics of these communities and the new data constitute a valuable contribution for the understanding of the functioning of the Adriatic ecosystem, the manuscript requires a careful revision addressing several important issues:

1. The word “mesoscale” in the title and in the objective is misleading, as no evidence is presented on hydrographic features or dynamics (i.e. currents, fronts, eddies,…) characterising the different subareas or were directly related to the described plankton assemblages. As the study conclusions are limited to large subregions, mostly related to the fishery management, the title and the objective should be more precise in this regard (e.g. Differences in taxonomic and trophic mesozooplankton assemblages across the Adriatic basin…).

Authors: Thanks for the observation, we agree and change the title accordingly “Differences in community composition and food web structure of mesozooplankton communities across the Adriatic basin (Mediterranean Sea)”

AR1

1. The claim that the study is relevant for the whole basin is not entirely supported by the data. The samples were collected on mostly the southern coast, with most of the stations on shallow depths (< 50 m) and none of the stations were located in the deepest waters (>200 m). The study characterized differences between inshore and offshore plankton and also between some subregions. The latter, initially defined from fishery survey areas, were subsequently grouped in the different analysis. However, because the limitations in the sampling, the different zones finally considered for the analysis need to be clarified. In the current version of the manuscript, the initial expectation of having 4 geographic subareas and two major depth categories (Fig. 1) is dismissed in the subsequent analyses. It would be appropriate to define the final analysed regions from the beginning by providing clearly the reasons for grouping the “fishery” areas and use an specific, more intuitive naming (e.g. North, Central, South) instead of the non-intuitive original code names (GSA17N, GSA18,…). Also, the variables used for supporting the groupings must be detailed (e.g. L 129-131), as well as the criteria for the inshore vs. offshore classification (L 176).

Authors: we agree with the reviewer concerning the lack of specifications in the abstract about the surficial “nature” of our samples. The MEDIAS survey effort, the samples came from, is concentrated to the epipelagic zone and thus no samples below 200 m are usually collected (we added this clarification in the abstract and throughout the text). Concerning the spatial effort, this included, samples collected across the entire basin, on the western side, as indicated by haul points in figure 1. regarding the sub-areas we agree with AR1 that the used of fishery subdivision could be misleading and thus we provided a clear rationale for the use of the three areas which are the object of the following analyses from the beginning, as suggested by AR1. In the revised version we’ll also detail the variables used for supporting the groupings, as well as the criteria for the inshore vs. offshore classification.

AR1

1. The organization of the manuscript must be improved. There is methodological information among the results (e.g. co linearity tests L 298-300; acidification test L 307-310), excess of auxiliary tables that could be safely moved to supplementary information (e.g. Tables 1 to 3, table 6), results among the discussion (e.g. L 421-424; 427-429), and analysis not well justified (e.g. PERMANOVA on untransformed data in L 174-177 and later on transformed data in L 182, a priori classification in trophic groups in L 209-213 and cluster in Fig. 4). In addition there are several inaccuracies and inconsistencies in the naming of variables and data through the text and tables (e.g. taxa with unknown trophic group = “Unk” or “?”).

Authors: we wish to thank AR1 for his/her indications about ms organization improvement. We’ll carefully revise this aspect in preparing the revised version. Auxiliary tables (1-3 and 6) will be moved to Supplementary materials, as requested. inaccuracies and inconsistencies will be carefully checked and corrected.

AR1

The abundance and biomass comparisons are made on data averaged in the water column (i.e. N or B / m3). Given the difference in the water column depths sampled in the different stations this approach tend to reduce the importance of offshore stations as the numbers are “diluted” in a large volume of water. In this case a normalization per unit surface (m2) may be appropriate (or at least explored). Also, the use of a logarithmic scale in the relevant plots (e.g. Fig. 2a) will facilitate the comparison of values.

Authors: we really thank the reviewer for this observation and we’re using the normalization to surface unit as suggested. We’re also changing the scale (to logarithmic) in the related plots.

AR1

1. The isotopic niche comparisons are flawed because of the lack of samples of species of low trophic position (TP<3) in one of the areas (Table 5). It would be more appropriate to limit the comparison of ellipses to all three areas but only for species with TP>=3 and the comparison of species to the ones having samples in all areas (e.g. C. helgolandicus, Chaetognatha, and Decapoda-zoea). In addition, the trophic position estimations are based on only one d15N measurement of G. tenuispinus from the central area that is applied to all areas. The authors must clearly justify the use of this baseline taking into account that the feeding of this species is ranked as “Unknown”. The use of a single baseline implies that the average source of N is the same across the basin which does not seem the case because of the inputs of the Po river (e.g. L 34-36, 125-126). Have the authors explored the possibility of using other values reported for zooplankton in the region?

Authors: We’re restructuring this part according to reviewer suggestions, i.e. considering only species in common to the three areas and also exploring the possibility to use other values reported for zooplankton in the region. However this last point could be difficult due to the scarsity of data in this sense and also to the possible bias generated by using different IRMS and labs as highlighted in Mill et al., 2007 (Mill AC, Sweeting CJ, Barnes C, Al-Habsi SH, MacNeil MA (2008) Mass-spectrometer bias in stable isotope ecology. Limnol Oceanogr Methods 6:34–39).

AR1

In addition there are several minor issues that need the attention of the authors, as exemplified below:

Authors: All minor issues have been addressed.

Dear Anonymous Reviewer 2,

we are very grateful for your precious comments which will allow us to better define mesozooplanktonic communities of the Adriatic basin in terms of assemblage structure, mostly liked to the peculiar oceanographic settings of the area. All your comments have been considering, in the preparation of the, edited version of the manuscript

Best regards Emanuela Fanelli

This paper describes the spatial distribution of mesozooplankton communities in the whole basin of the Adriatic Sea as well as the food structure of mesozooplankton based on isotope analysis. In general, the authors attempted to present the spatial differentiation of mesozooplankton community among the different areas of the Adriatic Sea. Although to be presented the zooplankton community for the whole basin is something rather new for the area, their findings regarding the observed differences in the mesozooplankton community between offshore and inshore among the areas it is something that is expected. What is missing is to investigate if the observed differences can be attributed to different mesoscale features existing in the area. However, the innovative part of this study are the results for the isotope analysis. The authors have used many species and they tried to find through the isotope analysis the food web structure of the mesozooplankton in the Adriatic. Although their findings are quite interesting and contributes with new knowledge especially regarding the findings from the isotope analysis, there are some parts in the methodology as well as in the results that the authors have to clarify before this article has the quality to be published. In the following notes, I will give some comments and suggestions on the different chapters that could help the Authors to improve their article.

In the abstract, a relative to the results conclusion is missing. Please add a more specific conclusion regarding to your findings.

Authors, Thanks we’re preparing a revised version of the manuscript amending all these points

Either in the Introduction or in the Methodology/study area description chapter, it would be helpful the authors to add a description of the hydrological conditions /mesoscale features/circulation that they existing in the Adriatic Sea during the sampling period.

Authors, Thanks for this suggestion, we’ll add this missing information.

Line 110. It seems that the selected areas are based only to the topograpfy and fishery management reasons. What about the existing circulation and mesoscale features of the area? Have you take into consideration other parameters as well for the division of the area?

Authors, The project this paper is based on is finalised to the assessment of smal pelagic fishes, this is the reason for our first chioce, however, according to your suggestions and also considerations from AR1, we’ll change such approach by considering oceangraphic settings of the area.

Line 116. Explain the reasons that you have done the zooplankton sampling in June/July since it is not one of the corresponding period to examine zooplankton in the open sea.

Authors, As reported in the previous reply, the survey of zooplankton was linked to the sampling and asssesment through acoustic methods of small pelagic fishes, thus the survey was linked to a favourable period for small pelagic sampling. We acknowledge your observation and add a better rationale for this choice, also in view of further analysis of that surveys’ samples aiming at assessing the importance of zooplankton for small pelagic fishes in the basin.

Line 123-131. Besides the selected oceanographic characteristics to separate the areas, have you tested if also other oceanographic variables such as T, S, O2, Chla and nutrients are significantly differentiated among them?

Authors, No we didn’t but thanks to your suggestion, we’re now testing these variables for differences with the appropriate statistical techniques.

In addition, what is the sampling bottom in areas GSA17S and GSA18? In the figures below there are six areas. It seems that the description of the selected areas is rather confusing. Thus, please clarify better how you have done the separation. It would be helpful if there is a Table to present the oceanographic characteristics and variables from the different areas as well as the significant differences among them

Authors, Thanks we’re preparing adn additional table with information about the  the oceanographic characteristics and variables from the different areas as well as the significant differences among them

Line 135-137. Some lines before (121-123) you have mentioned that you separated each sample in two subsamples. The first one is frozen and the second one is preserved in formalin. However, you preferred to do the identification of the zooplankton community in species level from the frozen samples. Can the authors explain why they have not chosen the preserved samples for their analysis, since the animals in the preserved samples will be in a better condition for their identification?

Authors, we need the samples for the isotopic analysis, of course we’d have analysed also the portion in formali, but we cannot then considered this portion for SIA, while doubling our effort. This kind of approach has been used before in other papers (Rumolo P., Fanelli E., Barra M. Bonanno A. et al. Trophic relationships of zooplankton in the Central Mediterranean sea: a stable isotopes approach. Hydrobiologia Special issue, DOI 10.1007/s10750-017-3334-9; Madurell T., Fanelli E., Cartes J. E. (2008). Isotopic composition of carbon and nitrogen of suprabenthos fauna in the NW Balearic Islands (western Mediterranean). J. Mar. Syst. 71, 336-345, Fanelli E., Cartes J.E., Rumolo P., Sprovieri M. (2009) Food web structure and trophodynamics of mesopelagic-suprabenthic deep sea macrofauna of the Algerian basin (Western Mediterranean.) based on stable isotopes of carbon and nitrogen. Deep Sea Research I, 56: 1504-1520); Cartes J.E., Fanelli E., Papiol V., Zucca L. (2010). Distribution and diversity of open-ocean, near-bottom macrozooplankton in the western Mediterranean: analysis at different spatio-temporal scales. Deep Sea Research I 57(11): 1485-1498; Fanelli E., Cartes J.E., Papiol V. (2011) Trophodynamics of zooplankton fauna on the Catalan slope (NW Mediterranean, etc.): insight from d13C and d15N analysis. Journal of Marine Systems 87: 79-89and although it’s true that not all the specimens can be identified at species level, this allows to analyse also the samples for SIA.

Line 138-139. Explain why you have chosen to use the wet weight biomass and no other expression of biomass like dry weight or in carbon.

Authors, as for the previous reply, samples were used for SIA, thus specimens were weighted after the identification, then some specimens were selected fior SIA while preserving the other material for potential further analyses.

Section 2.7. It would be good to compare the isotopic niche using the species found in all sampling areas. Clarify why you have taken Gaetanus  as a baseline, since you have found it only in one station. You should clarify why you made such a decision, otherwise it would be good for the baseline to use a common species throughout the study area. Use also recent publications for the eastern Mediterranean for your comparison and discussion.

Authors. Many thanks for this comment, according also to a similar comment from AR1, we’re restructuring this part according considering only species in common to the three areas, considerimng a common species to the three areas as baseline and and taking into account recent publications for the eastern Mediterranean for your comparison and discussion

Line 251-253. Do you mean here that there are not inshore-offshore differences between the same areas or between the different subareas? Please clarify your results. It would be more helpful to show in the Table the significant differences or not among the selected areas. It is difficult to follow the results.

Authors. Thanks, we’re amending the existing table, to better clarify our results, sorry for this.

Also the observed significant differences are only for the South to North areas? What about the central one?

Authors. Thanks, we’re discussing all the results in the amended version, including not significant ones.

Line 274-275. There is also a clear separation of GSA18 offshore from the other stations and the offshore stations of the GSA17N is close to those of the GSA17C-S according to the figure. Please explain better the results.

Authors. Sorry, as mentioned above, we’re improving this part on the results rpesentation and discussion.

Line 278-279. In the Figure 3 legend, what is the sub area 1??

Authors. Sorry, it was an oversight, this is the name given to the factor, now corretced in “sub-area”.

Section 4.2. Almost the whole paragraph should be moved to the results section in order to understand why you have made the selection of the areas.

Authors, sorry and thanks, this has been done in the revised version.

Line 431-432. DO is not only the major factor according to your analysis. Salinity and fluorescence have higher percentage. What about them?

Authors, we’re discussing also these other two variables in the revised version, many thanks for this suggestion.