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Reviewer 1 has provided a list of style suggestions and typos hat should be addressed during the proof stage.
[# PeerJ Staff Note - this decision was reviewed and approved by James Reimer, a PeerJ Section Editor covering this Section #]
[# PeerJ Staff Note: Although the Academic and Section Editors are happy to accept your article as being scientifically sound, a final check of the manuscript shows that it would benefit from further editing. Therefore, please identify necessary edits and address these while in proof stage. #]
The authors have addressed my previous issues. I only have a couple of style suggestions and typos at this point:
L. 21: “A larger role”?
L. 95: Remove “s” from “variations”.
L. 122: “Biotic components” sounds a bit odd to me. Maybe replace with “biota”? (Here and elsewhere in the manuscript)
L. 126: I suggest removing “biotic” before “communities”. (Here and elsewhere in the manuscript)
L. 302: Maybe specifically add that the condition for this: x<|2|.
L. 441: remove colon after “Actinobacteria”.
L. 444: Change “taxa” to “taxon”.
L. 448: Depending on the meaning of the sentence the colon after “taxa” might need to be removed. Are the specific taxa typical for New Zealand or is it typical for New Zealand that zooplankton taxa are dominating the epi (which seems a given when using COI)? I assume the first (in which case: no colon), but am not sure.
L. 511: Add colon after “lakes”.
L. 513: Remove colon before “may”.
L. 532: Remove “enough”.
L. 553: I think “this…” should be a stand-alone sentence.
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The authors adequately addressed the reviewer's concerns and the manuscript appears ready for publication.
Dear Authors,
I agree with the two reviewers. Please perform revisions and resubmit.
-The English used in this manuscript is clear and professional.
-The introduction and background are mostly well presented. However, I was missing some background regarding the importance of sediments and their communities for the ecosystem, given that the authors put a lot of emphasis on the added value of sediments to their analysis. What relationship do we expect between water column and sediment communities giving the sinking and resuspension of cells? How will selection pressures differ? In general, I wonder if the sediment communities represent ‘true communities’ of organisms living together or rather assemblages of organisms living in the sediments and cells which sank down from the water column. If the authors consider selection on the assembly level, the former would be directly selected on in the sediment and the later would be remnants of selection in the water column. I don’t think there is a perfect answer for this issue when studying sediments, but I think the authors need to discuss their hypothesis and findings in the light of this potential caveat.
-The structure and figures look good to me.
-The raw data (sequence data) and the ASV tables are missing.
-The research is original and within the scope of the journal.
-The research question is defined and relevant and fills a knowledge gap (sediment communities/ assemblies)
-The investigation is rigorous/ high technical standards.
-Method description: I found the design of the sampling a bit confusingly explained. Did the authors sometimes sample the epi- and the hypolimnion of the same lake? They indicate that they sampled below the thermocline for the chlorophyll and nutrient analysis, but no such samples are mentioned for the biological samples. If hypo and epi samples were collected for some lakes, were their communities analyzed together? I’m asking because I expect an inflated signal for variable selection if communities are compared between epi and hypo samples.
-The conclusions are well stated, linked to the research questions and supporting the results.
-The most basic level of the underlying data is missing (sequence data), ASV/OTU tables are missing, meta data is present, the statistics are appropriate.
-DNA data checks: Data deposition statement is missing, so access can’t be verified.
L. 97: Interesting to see human lake access as a source of stochastic processes (dispersal). What about associated deterministic processes (e.g., proximity to roads and built environments, pollution)
L. 117: Why is sediment more heterogeneous environment than water column? Integration of environmental factors over time? Geology?
L. 166: In addition to a surface water sample?
L. 260: “A stop codon of greater than two frame shifts”? Do you mean “a stop codon or a frame shift”?
L. 364: Can assembly processes be reliable estimated if the communities are undersampled?
L. 388: Do environmental factors (e.g., TN and TP) also differ with ease of access? This might indicate that human access relates to lake pollution, resulting in heterogeneous selection.
L. 430: I find this paragraph unclear. Were Boeckella expected to be present in both the SPeuks and the LPeuks? Is the idea that Centropagidae were misclassified as (non-native) Diaptomidae because that’s the closest-related 18S ref sequence available?
L. 442: I suggest to move this part of the paragraph introducing the impact of different zooplankton species to either the introduction or the beginning of the paragraph.
L. 484: … or that undersampling of the communities precludes the detection of the processes.
"Sequence reads were deposited in the NCBI short read archive under the accession number: PRJNA750120, PRJNA762383 and PRJNA853061." is mentioned in the submission details but this information does not appear in the manuscript.
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The manuscript by Pearman and collaborators deals with the characterization of distribution patterns and assembly processes of planktonic and sediment-dwelling freshwater bacteria and eukaryotes in selected New Zealand lakes. The authors’ approach is interesting and they make a convincing case about the dichotomy in planktonic vs sedimentary community assembly as well as the significance of anthropic effects on dispersal. Some minor issues ought to be addressed before publication.
Lines 190-194: why are small and large planktonic eukaryotes collected separately in 20 and 40 um fractions as well as processed and analyzed separately but sediment surface eukaryotes are not?
Lines 240-252: was a quality threshold used?
Lines 278-280: “rarefaction curves were constructed” – were amplicon counts normalized by rarefaction and if so, to how many? Otherwise, how was the ASV table normalized?
Lines 323-325: how many permutations were used?
Lines 334-337: what did the rarefaction analysis consist of? Was a statistical test applied to ascertain whether saturation was reached to a specific degree of confidence? Visually, the bacterioplankton and sediment surface eukaryotes subplots suggest ASV counts could increase by about 100 for each with twice their sequencing depths. It is however fair to conclude sampling depth was only insufficient for planktonic eukaryotes.
Lines 511-533: it may be excessive to ask for this to be included in the analysis, but what effect would connectivity have on distribution patterns and assembly processes as characterized in this study? For example, if a lake without access is located 10 km downstream on a river flowing from another lake with walking access? Are there enough lakes connected to each other in the present dataset to investigate this issue?
Lines 547-550: the two first sentences of the conclusion are quite general and do not contribute much to the narrative of the paper.
The conclusion ends somewhat abruptly.
Figure 1: perhaps specifying the unit for the axes, i.e. "Latitude (°)".
Figure 2: what do error bars in figure 2 represent? It could be mentioned in the figure caption.
Figure 3: effective visualization. Well done. Does the width of the bar for the microbial groups also represent something?
Figure 4: are the grey areas 95 % confidence intervals on the linear regression curves? This information could be added to the figure caption.
Figure 5: how much correlation is there between access levels and environmental variables? It is difficult to visualize gradients when there is one factor provided but the latter is not associated with clear groupings. Although it would result in cluttered plots, it could be interesting to see environmental variables fitted to the NMDS, for example using envfit() from vegan. If informative, a supplementary figure could be included, presenting an ordination of the sites by environmental variables with the access level factor used for color coding data points.
Supplementary tables 2 and 3 titles/descriptions are mixed up.
There is missing data for water temperature and dissolved oxygen at the bottom for Lake Mapourika. How were those missing observations handled prior to computing the environmental variables distance matrix?
General comment on English: punctuation can be improved.
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