Biogeochemical Responses and Seasonal Dynamics of the Benthic Boundary Layer Microbial Communities during the El Niño 2015 in an Eastern Boundary Upwelling System
, Marcela Cornejo-D’Ottone 3,*, Eulogio H. Soto 4,5, Eduardo Quiroga 3, Guillermo Alarcón 3,5, Daniela Silva 1, Carla Acuña 1 and Nelson Silva 3Round 1
Reviewer 1 Report
This manuscript traces the dynamics of physicochemical parameters and diversity of archaea and bacteria during an El Niño year in an upwelling zone. The topic is fascinating, and the methods are generally sound, however, some major flows make not only the endorsement but the review difficult.
The paper requires major language editing. I only give a few examples of language corrections needed for the abstract (see minor comments). However, this has to be done throughout the text. Please consider consulting a language editor before further processing of this manuscript.
I didn’t find the supplementary files. This hinders the proper evaluation of this paper, as many important details are presented in the supplement.
I had difficulty finding from which water depth the samples for molecular analyses were collected, and how many sediment samples were analyzed. Were there any replicates? The ENA archive is missing metadata indexing the evaluation of reads.
The sample size seems to be very limited, and it is not clear how the statistical comparisons are feasible.
There is no need to compare sediment vs water communities, rather discuss the temporal changes in light of physicochemical parameters.
Minor comments:
Please consider rephrasing the title, the structure of the sentence is odd – maybe something like “Biochemical responses and dynamics of the benthic boundary layer microbial communities during…”. Also, the EBUS acronym is unnecessary in the title.
L22: Please expand the acronym ENSO (also correct in the keywords).
L23-24: Please rephrase “The oceanographic dynamic, pelagic and benthic microbial changes” – not clear what it means. “i-tag” is rarely used, better “amplicon sequencing of the 16S rRNA gene”. Instead of mentioning the method in parentheses, it is better to just state the method, e.g. “we identified changes in microbial communities using amplicon sequencing of the 16S rRNA gene…”. In general, it is better to avoid using parentheses, but just say directly what is meant (e.g., line 30, “putative ammonia oxidizers Thaumarchaeaota…”.
L28: Please rephrase the whole sentence – it is odd. Also, H’ = Shannon’s H’, please state the statistical power of the comparison. Why is this stated in the abstract, and even not mentioned in the main text?
L29: For most of the mentioned lineages, modern taxonomic affiliations were curated. Please consult here: https://gtdb.ecogenomic.org/
L72: Candidatus in italics and the genus name in normal font.
Stopped correcting here…Please revise throughout the paper.
Author Response
Reviewer Comment
This manuscript traces the dynamics of physicochemical parameters and diversity of archaea and bacteria during an El Niño year in an upwelling zone. The topic is fascinating, and the methods are generally sound, however, some major flows make not only the endorsement but the review difficult.
The paper requires major language editing. I only give a few examples of language corrections needed for the abstract (see minor comments). However, this has to be done throughout the text. Please consider consulting a language editor before further processing of this manuscript.
I didn’t find the supplementary files. This hinders the proper evaluation of this paper, as many important details are presented in the supplement.
Answer.
The manuscript was edited considering the reviewer suggestion and English editing was performed. We are sorry that the supplementary files were not found by the reviewer. We did upload them and ask the editorial office, since is not possible to submit them embedded in the same word file.
I had difficulty finding from which water depth the samples for molecular analyses were collected, and how many sediment samples were analyzed. Were there any replicates? The ENA archive is missing metadata indexing the evaluation of reads.
The sample size seems to be very limited, and it is not clear how the statistical comparisons are feasible.
Answer: The project budget involved a seasonal oceanographic study 2014 – 2015 with emphasis in bottom layer and sediment characterization. The oceanographical data presented here include seven sampling months (June-14, October-14, January-15, April-15, August-15 and December-15) representative of seasons, associated to nutrients, greenhouse gases (carbon dioxide, methane, and nitrous oxide) and sedimentary characterization such as organic matter quantity and quality indicators besides other parameters helping to describe sediment conditions in particular for the year 2015.
The amplicon 16S rRNA sequencing data involves 14 sequencing analyses using two set of primers, for bacteria and archaea. We include the indexing in the new manuscript. The data is limited to one replicate associated with benthic boundary layer characterization focused on the activity of bottom water samples based in cDNA, and three sediment based on DNA (Table S4, supplementary material). Bottom water samples were further analyzed to evaluate specific activity of nitrifying assemblages considering its expected connection with oxygenation and potential nitrous oxide contribution. This study represents the first using the benthic boundary layer microbial community in the upwelling area off Valparaiso, however our results are supported by previously published data associated with longer time series in upwelling areas further south, helping us to put in perspective our short time-series biogeochemical dynamics. Statistical contribution was mainly based in SIMPER analyses for microbial communities considering upwelling versus non-upwelling periods.
There is no need to compare sediment vs water communities, rather discuss the temporal changes in light of physicochemical parameters.
Answer. The comparison was made since the emphasis of the paper was a benthic boundary layer bottom water active community and their potential source associated to surface sediment communities. In this new manuscript we explain this in a better way and delete paragraphs only based in the comparison.
Minor comments:
Please consider rephrasing the title, the structure of the sentence is odd – maybe something like “Biochemical responses and dynamics of the benthic boundary layer microbial communities during…”. Also, the EBUS acronym is unnecessary in the title.
Answer: We changed the title following the reviewer suggestion.
L22: Please expand the acronym ENSO (also correct in the keywords).
Answer: We expanded the acronym following the reviewer suggestion.
L23-24: Please rephrase “The oceanographic dynamic, pelagic and benthic microbial changes” – not clear what it means. “i-tag” is rarely used, better “amplicon sequencing of the 16S rRNA gene”. Instead of mentioning the method in parentheses, it is better to just state the method, e.g. “we identified changes in microbial communities using amplicon sequencing of the 16S rRNA gene…”. In general, it is better to avoid using parentheses, but just say directly what is meant (e.g., line 30, “putative ammonia oxidizers Thaumarchaeaota…”.
Answer: The abstract was rewritten.
L28: Please rephrase the whole sentence – it is odd. Also, H’ = Shannon’s H’, please state the statistical power of the comparison. Why is this stated in the abstract, and even not mentioned in the main text?
Answer: We agree and delete this comparison.
L29: For most of the mentioned lineages, modern taxonomic affiliations were curated. Please consult here: https://gtdb.ecogenomic.org/
Answer: We decided to use the taxonomic affiliations following the database used and mention current name for interested reader.
L72: Candidatus in italics and the genus name in normal font.
Answer: We change this throughout the text
Stopped correcting here…Please revise throughout the paper.
Reviewer 2 Report
The authors present data on the oceanographic dynamics, pelagic and benthic microbial changes and active functional nitrifying groups during 2015 in an Eastern South Pacific coastal zone.
Although the data is interesting, the paper, in this present form suffers from serious shortcomings.
The first is that the time series is very limited to make some of the conclusions presented. The authors present data from a few discrete sampling but make assumptions over the time variation of the measured variables that are basically not valid (for example, Figure 1 shows time data based on 5 time points, assuming the variation in the data between such separate discrete samplings is too bold). This results in an over-interpretation of the results. I find somewhat daring to call such dataset a time series.
Moreover, the authors attribute some of their observations to a climate phenomenon, the El Niño. However, there is not enough data to support their conclusions. Seasonal changes are large in marine ecosystems; more data is needed, in particular from other years for comparison to make some conclusions.
Overall, the significance of the question being posed is high but authors need to be more rigorous with the presentation and interpretation of their results.
The quality of the writing also needs to improve, there are many grammatical and formatting errors (including that species names are not presented in italics) throughout the manuscript. The way the microbiological data is presented is confusing, it is unclear what data comes from RNA and which from DNA, and whether the water and sediment data can be compared.
Overall, I do not recommend this paper for publication in the present form. Given that the data is interesting, I would suggest to present it in a more rigorous and rewrite the paper
Author Response
Reviewer comment
The authors present data on the oceanographic dynamics, pelagic and benthic microbial changes and active functional nitrifying groups during 2015 in an Eastern South Pacific coastal zone.
Although the data is interesting, the paper, in this present form suffers from serious shortcomings.
The first is that the time series is very limited to make some of the conclusions presented. The authors present data from a few discrete sampling but make assumptions over the time variation of the measured variables that are basically not valid (for example, Figure 1 shows time data based on 5 time points, assuming the variation in the data between such separate discrete samplings is too bold). This results in an over-interpretation of the results. I find somewhat daring to call such dataset a time series.
Answer: We used this kind of plots to make it easier to evaluate changes, not to give the of interpolating data associated with non-sampled periods. To avoid this kind of confusion we changed the graphs and only profiles were included in figure 1 and 2. Our sampling consisted in two representative months for 2014 June (winter), October (spring) and four representative periods January (summer), April (fall), August (winter) and December (late spring) for 2015. These represent a seasonal sampling therefore we add the word “seasonal” to our time series and mention the months for clarity. In this new manuscript we try to avoid over-interpreting our results and the manuscript was changed accordingly. However, despite the time series is short, our results were comparable with monthly time series in an upwelling area further south (off Concepción), helping us identifying similar responses and thus give support to our own representative months observations which are obviously “limited” compared with other time series. Time series are hard to accomplish, and this is one of the first in Valparaíso area including both benthic and pelagic information and the only one including information about microbial community during El Niño year. We think that reporting this in a broad perspective journal special issue such as Water will be important to bring attention to some findings such as the potential response of microbial community to oxygenation in the benthic boundary layer (bottom water-sediments), and its relationships with greenhouse gases. Thus supporting possible new funding to carry out longer timeseries.
Moreover, the authors attribute some of their observations to a climate phenomenon, the El Niño. However, there is not enough data to support their conclusions. Seasonal changes are large in marine ecosystems; more data is needed, in particular from other years for comparison to make some conclusions.
Answer: The reviewer is right about climate phenomenon and we did not intent to be so speculative. However, satellite images in supplementary files are used to support the influence of El Niño in the study area considering hydrography and published information in the study area and other upwelling zones. We tone down and changed the conclusion.
Overall, the significance of the question being posed is high but authors need to be more rigorous with the presentation and interpretation of their results.
Answer: Thanks for your comment; we try to be more rigorous, in the presentation and interpretation. As mentioned, we changed the ODV figures including profiles and add all the data in the supplementary analyses for biological data available. Labels of the data origin (months sampled) were added or mentioned in the figure legends, and we focus the discussion to our seasonal findings.
The quality of the writing also needs to improve, there are many grammatical and formatting errors (including that species names are not presented in italics) throughout the manuscript. The way the microbiological data is presented is confusing, it is unclear what data comes from RNA and which from DNA, and whether the water and sediment data can be compared.
Answer: We change species names and explain better the microbiological data, including this information in the figures in the new manuscript version. We check the material and methods and paraphrase some paragraphs to clarify the origin of the sample’s cDNA versus DNA. Overall, I do not recommend this paper for publication in the present form. Given that the data is interesting, I would suggest to present it in a more rigorous and rewrite the paper
Answer: The idea of comparing the active microbial communities from the bottom water with the surface sediments is because both compartments are expected to share some key groups due to continuous exchange as nutrients do (sediment – water interface), that is the vision of the benthic boundary layer. In fact, our findings indicate that the active microbial community in the water is present in the sediment as well. We think that this is an interesting result to mention. We rewrote many area of the manuscript and consider the reviewer general suggestions to avoid overinterpretation. An English language specialist edited our manuscript.
Round 2
Reviewer 2 Report
I had review a previous version of this manuscript. The authors have adressed the suggestions and presented the manuscript in an improved form.
