Review of Burian et al., Drivers of microbial food-web structure along productivity gradients. MS RSPB-2022-1288

General

This paper combines intensive in-lake analyses, a survey of regional lakes, and a substantial meta-analysis of published literature to investigate the controls of viral particle:heterotrophic bacteria (VP/HB, or V/B hereafter) and HB/Chlorophyll (B/Chl hereafter) ratios. The authors take an interesting statistical approach with a combination of structural equation modeling and various regression-based approaches. Overall the findings appear solid – there are strong relationships between viral and bacterial abundances, which may vary as a function of ecosystem production. However, I am left with the impression that the paper is less accessible to a broad audience than would be necessary for a general readership such as PRSB. As part of this I was like to see a better rationale for the comparison of highly productive soda lakes and marine ecosystems (why these systems). As well, I am concerned about the use of turbidity as a common metric for particle concentration, particularly in cross-ecosystem comparisons, without some means of also correcting for the algal density. Additional details and finer-scale comments for the authors are provided below, arranged according to the line number of the original submission.

Specific

1. Perhaps my most significant comment is that I think the paper is pitched too closely to a microbiology audience. While that might be fine for specialist outlets for aquatic microbiologists, I think it leaves the paper a bit less accessible than it should be for a journal with a broader readership. For example, despite being a limnologist who works on eutrophication issues, I found that I lacked to context to assess many statements in the paper, particularly in the Discussion. I don’t think this requires a lot of modification, rather just that the authors put themselves in the shoes of someone who is not a virologist or aquatic microbiologist. Below I identify a few instances where further explanation or context would be helpful.

2. l. 47-51. The centerpiece of the paper is the presumption that ratios of V/B or B/Chl are truly insightful for the study of aquatic microbiology. While I don’t doubt there are some important features, this seems too presumptuous or overstated (e.g., l. 88-89). As an analogy – limnologists spent a decade looking at food-web (trophic) cascades as a means of regulating primary production and, while ratios of zooplankton to algae are interesting, they never provided key insights to the conditions under which grazing was an critical regulatory project – for this you needed species identify, nutrient status, physico-chemical controls etc. I guess what I am saying is that it would be nice to have a clear statement of when or where the ratios provide critical insights as abundance ratios are not typically ‘transformative’ in many branches of environmental science.

3. As an aside from a non-expert, I am curious why virus/Chl ratios are not investigated. Given the importance of cyanobacteria in productive freshwaters (e.g., Fig. 1a, b), this seems like an overlooked avenue of investigation. Is it because viral research has progressed more rapidly in marine systems, where cyanobacteria are not normally predominant? It would seem that considering the relationship of V/Chl as well as V/B might provide insights on whether it’s just the bacterial density that is regulating viral presence, or whether there are other environmental controls. It also seems more symmetrical to my mind (look at all ratios).

4. l. 88-119 and methods. I am a little uneasy with the use of hypereutrophic soda lakes as a benchmark for the paper without actually making them the central focus of the conclusions (which are more based on the site-to-site comparisons). In particular, the comparisons with marine systems seem slightly arbitrary – other than the systems both being saline and aquatic, there would be very little that I expected to be similar between the habitats, including ecosystem fundaments such as ionic composition. I can see a very solid paper focusing on the soda lake monitoring and its integration into the survey of other African lakes, but I find that the literature review feels kind of “bolted on” as a separate issue. Perhaps this is just my lack of familiarity with viruses and heterotrophic bacterial ecology, but I think the authors could consider whether they actually have papers linked together and whether one paper would be more compelling to readers.

5. l.117-119. Based on a critical review of the literature in the Introduction, I would like to see more specific hypotheses. What do we know about soda lakes which may (or may not) lead to predictions about other ecosystems? This may help address point 4 above.

6. l. 168. Neither paper would appear to have the code for the “custom SEM” procedure – this should be provided in an on-line archive if key numerical procedures are supposed to be open access.

7. l. 206-211. Given the density of cyanobacteria (Fig. 1), I am concerned with the use of turbidity as an independent metric of particle density in the water. Perhaps this would be suitable in unproductive ecosystems, I think it’s problematic in hypereutrophic lakes where much of the physical turbidity would be derived from phytoplankton (and especially when comparing broadly across many ecosystem types). Given that the negative relations between V/B and particle density are driven by very turbid (productive?) systems, I recommend unpacking the relationship between phytoplankton and density. One option would be to look at the residuals of the relationship between turbidity and Chl a as a metric of non-phytoplanktonic particles.

8. l. 234-248. It would be useful to see the regression relationships mentioned in the text also presented in an on-line Appendix. I think this is useful given the centrality of the regressions to the paper (other figures).

9. l. 309-324. Given the unknown nature of the ionic composition and other chemical features of the intensively studied soda lakes, I find these paragraphs are overly speculative.

10. l. 326-376. This is one of the sections where provided the readers with a bit more context might make the explanations more accessible to readers.

11. l. 377-394. Again, this section is very speculative and difficult to evaluate based on the data presented. I’m not certain the top-down, bottom-up debate is really central to the present manuscript.