Review of “Effect of hydro-climate variation on biofilm dynamic and impact in intertidal environment”

Review date: June 2, 2022

Ethics: This is my first review of the manuscript and I identify no conflicts of interest.

Review by: Matthew Hiatt

Summary: This manuscript presents an analysis of the influences of biomass and biostabilization on 1D tidal morphodynamics. A validated hydro-morphodynamic model is presented and amended to include the effects of biostabilization on long-term (~10^4 tidal cycles) tidal channel morphology and depositional/stratigraphic patterns. The influences of hydrodynamic disturbances (frequent, infrequent, small, and large) on biofilm development are also assessed alongside the effects of temperature, biofilm development depth, and biofilm growth rates.

Assessment: Overall, the topic is of interest to readers of ESurf. The paper presents a novel combination of models on an emerging topic addressing the role of smaller scale biological processes on channel-scale geomorphology. This topic fits the journal quite well and is timely. The writing is overall good and clear, albeit in a draft that has many small grammatical mistakes throughout. However, that does not impact the understanding of the science, but certainly needs to be addressed. The motivation and approach to the problem are well-reasoned, but the validity of the biostabilization model is not addressed (see Major Comment 1). The sensitivity analysis is easy to understand when the results are presented, but it is not at all clear what will be tested when reading the Methods section (see Major Comment 2).  Alongside these it is unclear from a physical perspective, what the hydrodynamic disturbances represent (see Major Comment 3 & 4). That being said, the results section of the paper quite clearly lays out the results and the outcomes are easily understood. I recommend that there be significant revisions to the paper, primarily focusing on validation/justification of the biostabilization and biofilm growth models (it is mentioned they are validated but with what data?) and clarity surrounding the sensitivity analysis scheme and the physical manifestation of the hydrodynamic disturbances.

Major Comments:

One concern is that the biofilm-dependent erodibility model and the model describing the biofilm biomass dynamics (i.e., all of section 2.3) does not seem to have any backing by observations or data other than the reference to Friend et al. (2002) in line 245. This reference identifies the temperature controls on the growth of MPB. Nevertheless, there is no evidence presented that the behaviors displayed in Figure 2 are representative of reality. They may very well be, but the evidence is not explicitly provided, calling into question what the sensitivity analysis results mean (e.g., if the base parameters in the model are not representative, what does the sensitivity analysis teach us?). That does not mean, in my opinion that the analysis is invalid, but I do think that the authors have an opportunity to more clearly and convincingly address the validity of the models presented in section 2.3. This will enhance the reader’s confidence in the results presented in the following section.

It is unclear to this reviewer the ranges of the sensitivity parameters being tested. I see in lines 290-296 that a number of different model parameters are being tested, but I have no clear understanding of how they will be modulated, how many model runs will be performed, if parameters will be tested in isolation or a scenario format. Essentially, I have no idea what to expect to see in the results of than some form of model results. The manuscript would benefit from a clear description of the testing scheme. It’s fairly clear after reading the results, but comprehension would have increased with a table of tabled parameters in the methods or perhaps pulling Fig.A3 into the main text to show the tested parameters.

For the “strong” and “weak” disturbances, it would be useful to provide descriptions of what types of events these are representing (storms? Regular tides? Especially high tides?) to go alongside the shear stress values presented. It’s also unclear to me whether the intervals of disturbance chosen are representative of anything “real”. What does 15/5 day intervals represent? Is it an arbitrary selection?  Or is this a spring and neap cycle? I understood that the tidal forcing was only semidiurnal.

How are the hydrodynamic disturbances imposed on the model? Are these done by drastically increasing water level at the seaward boundary or is there a momentum component? Or is there wind in the model? Over  a small domain (25m), I would doubt it. I think this confusion could be rectified by addressing the previous comment and then briefly describing how the disturbances are implemented.

Minor Comments:

Lines 11-14: There is something wrong with grammar of this sentence. The list of metrics ( or perhaps those are the tuning parameters for the sensitivity analysis – it’s not clear) isn’t explained. I think I get the point but the sentence needs to be restructured for clarity.

Line 18 & 317 & 465 & 595: Can’t say “on the other hand” without a previous sentence saying “on one hand.” It’s a pet peeve of mine :)

Line 22-23: rephrase to “…predict estuary development and mitigate coastal erosion”

Line 40-48: I’m wondering if the authors could add a quick comment somewhere in here about the global ubiquity of MPD and EPS on intertidal and subtidal channels. Is it present throughout the world? If so, how prevalent is it?

Grammar in Section 2.3 and beyond: I’m noticing several sentence fragments, missing punctuation, issues with parentheses, and noun-verb plurality disagreements. I can still understand the text but it’s distracting. (Examples include lines 247-249, line 245, line 221, line 249, and further along with grammatical errors in line 296, line 299, lines 347-352, among others). I stopped noting them after about line 350, but to be increasing in frequency as the manuscript goes on.  

Lines 347-350: A reference to Fig A3 is appropriate here. It took me a while to figure out what this sentence meant until I search through the appendix.

Figure 4: The inset figures in c, g , and k are extremely small. I would also suggest using the figure itself to highlight assumptions for each row. Perhaps this means labeling them in the figure by highlighting the rows, or similar (this is already done for the columns). With a full page figure, I keep having to scroll back and forth between the figure and the description to figure out what I’m looking at.

Line 449: I know it’s not used in the simulations shown in Figure 6, but I’m still very unclear about what “high hydrodynamic forces” means from primarily the physical perspective ( I understand the quantitative shear stress side).

Lines 473-474: “This result in a more stable bed, morphological changes occur in a longer timeframe and,  by the end of the simulation, it does not reach an equilibrium condition”…I don’t understand this argument. Why would it reach and equilibrium state along the same timeline as the simulation not including the biomass growth and biostability? It seems they are two entirely different simulations that can certainly be compared, but I don’t think it’s a foregone conclusion that they should reach the same steady state condition simultaneously. However, it does appear in Figure 6c that it is approaching some type of steady state, albeit potentially significantly more slowly than in Figures 6b or d. Were the simulations extended out beyond ~10^4 tidal cycles to verify it does not reach an equilibrium state?

Line 529-530: I’m wondering what the justification is for extending the results presented here to estuarine stability. The results presented only test the effects of disturbances and biomass growth on tidal channel morphology in one dimension. This cannot account for the myriad factors contributing to whole estuarine morphology. In fact, the model presented here does not even model an estuary at all, but a single tidal channel. The connection seems tenuous. I think the authors should either omit this point of discussion or stringently justify the extension to whole-estuarine morphology.

Line 543: The line here states the model is validated for temperate areas. I don’t see any comparison to data. Was it validated in another paper? I looked throughout the manuscript and didn’t find any mention of this. This is the only mention of validation is in regard to the morphodynamic model along (Appendix Figure A1) This bring me back to the Major comment #1.

Appendix Figure A3: This is not discussed at all in the appendix text.

Line 630: This is a sentence fragment or something.

Lines 577-649: I think this section can be significantly shortened. There is a lot of addition literature review here with only a few lines relating the material studied in this paper to known processes/effects published in the literature. I encourage the authors to trim this down and focus more on contextualizing their results within the current understanding of biostabilization and the state of modeling such processes (as alluded to in 616-617).

Effect of hydro-climate variation on biofilm dynamic and impact in intertidal environment

Bastianon, Hope, Dorrell, and Parsons

Summary of Manuscript:

This study aims to develop a 1D model morphodynamic model that includes the role of biofilms. The authors couple (and adjust) existing models of morphodynamics and biofilm growth to assess how biofilms affect the evolution of tide-dominated channels. The model results demonstrate the importance of growth parameters (growth rate, temperature) on morphodynamic changes. Furthermore, through the many iterations of the model, the results show that biofilms increase the time needed for the profile to reach equilibrium, and result in different profiles.

Scientific Significance:

This study is novel in that it couples existing models of biofilms and morphodynamic evolution to understand how biofilms affect a sandy channel. This is new and different from (the few) previous modeling studies of biofilms and morphodynamics, and provides interesting insights into the biogeomorphic processes that exist in probably all estuaries and are typically neglected.

Scientific Quality: The model approach is of high quality.

Presentation Quality: For better readability, and therefore greater paper impact, I have several suggestions for cleaning up figures and making them more legible. Furthermore, I think the paper could be improved in the format/structure – right now a lot of it reads more like a report rather than a complete story answering the scientific question. I think the results could be shortened in order to emphasize the take-away messages of the study – that biofilm growth and seasonality are important for understanding biomorphic systems.

Comments:

1. What about seasonal variability in erosive events? I don’t think it is necessary to include new model runs of this in the manuscript (you already did a lot of model runs!), but I think it would be worth discussing the impacts of a system that has seasonal variability in storms – where the two different disturbance scenarios you describe may both exist within a year but at different times.
2. The authors do a good job describing the relationship between biofilm biomass and chla, but neglect to really mention EPS production directly. I would recommend to add a paragraph to the introduction that discusses the relationship between EPS and erodibility (which is much stronger than the chl a – erodibility relationship, and has a stronger process-based explanation), and why you chose to model chl a instead of EPS production. There are some particularly interesting studies that point out that EPS production can be linked to other factors (like nutrient availability, biofilm stress, see Ruddy et al. 1998, Smith and Underwood 2000, Underwood 2002, Orvain 2003, Orvain 2014, Hubas 2018) that may effect erodibility. While I think modeling chl a/biofilm biomass as a proxy for erodibility is fine (and standard practice), I think mentioning these limitations is important.
3. Is there residual EPS in the sediments? Once there is erosion, should the sediment really return to an abiotic state? I think this is an assumption that affects your results (also the results of Mariotti and Fagherazzi 2012, Pivato et al. 2019, and others). I think this merits some discussion in the text. There is some evidence that even after erosive events, some remnants of biofilm or EPS may lead to faster biofilm establishment (Chen et al. 2019) or changes in erodibility after repeated erosion (Valentine et al. 2014).

Figure Comments:

I think one big area for improvement in this paper is in the figures. There are a lot of figures with a lot of panels and they are hard to digest as a reader. I have some suggestions about how to improve them to make your arguments stronger! I hope they are helpful.

Generally, I think all figures that showed the evolution of the profile had too many lines which made it difficult to read the figure.

Figure 1 – In the caption, it should be “represents”. Additionally H is not listed in the caption and the dots on the figure (representing grain size?) are not labeled.

Figure 3 – On the x axis, you may consider labeling the months instead of using days. You reference the months in the manuscript, and it takes work for the reader to translate that to days quickly.

I liked that you labeled the two columns on the figure; I think you should also label the rows more clearly (maybe a label that encompasses the first three rows that says “Growth Rate Parameter” and one that encompasses the later two rows that says “Sediment Temperature”). I think this would help with the readability of the figure. The info is in the caption, but I think it would be more effective to put more labels on the actual figure.

I typically agree that the y axis in all panels should be the same, however, it is impossible to see that there is any growth in panel a (as suggested in the text). I’m not sure what to do about this.

You also have the potential to minimize the empty space between the panels in order to make each subplot larger, which I think would look better but use up the same amount of space.

Figure 4: I would label the rows of panels, like you did with the columns. It is a lot of subfigures! I liked how you labeled the mean water surface elevation and initial bed in panel a – that was very useful. I did have some difficulty with the profiles due to the number of lines displayed on each figure, I recommend reducing the number of profiles visualized. I may also try other colorbars, as the yellow was particularly difficult to see.

This is a judgement call on your part, but I would remove the tiny subplots within panels c, g, and k. They are very small and not readable. I understand you were trying to point out what the row represented, but I think simple labels (like how you did the columns) would be more effective.

Figure 5: Again, I recommend labeling the columns or the panels with what they represent (small, medium, and large growth rates) to make for easier reading.

Figure 6: Sorry for the repetitive comment (hopefully it is easy to do at least) – please add the labels for the temperature “treatments” for the different columns on the figure.

Figure 7: Please label the panels (or columns) with the alpha value used.

Specific Comments:

Line 96: Should be “tidal dynamics”

Line 159-160: remove the and between tidal currents and sediment erosion.

Line 356: should be “uniformly distributed”

Line 356: I think you mean the left two columns? (instead of panels)

Line 357: You refer to the fact that some studies have found biofilms in deeper waters, which I agree! You reference some of these papers later in the paper, but I think you should add citations when you say “as it has been also suggested in the literature (cite xx)”. 

Line 446: Should be “biofilm growth differs”

Line 448: Should be “affect” instead of effect

Line 450: I think neglect is not the right word here. Does absent or negligible fit better?

Citations:

Chen, X., Zhang, C.K., Paterson, D.M., Townend, I.H., Jin, C., Zhou, Z., Gong, Z., and Q. Feng, 2019, The effect of cyclic variation of shear stress on non-cohesive sediment stabilization by microbial biofilms: the role of “biofilm precursors’, Earth Surf. Proc. Land., 44: 1471-1481.

Hubas, C., Passarelli, C., and D.M. Paterson, 2018, Microphytobenthic Biofilms: Composition and Interactions, in Mudflat Ecology, ed. PG Beninger, Springer, 63-90.

Mariotti, G., and S. Fagherazzi, 2012, Modeling the effect of tides and waves on benthic biofilms, JGR: Biogeosciences 117: G4.

Orvain, F., Galois, R., and C. Barnard, 2003, Carbohydrate production in relation to microphytobenthic biofilms development: an integrated approach in a tidal mesocosm, Microbial Ecology 45: 237-251.

Orvain, F., De Crignis, M., Guizien, K., Lefebvre, S., Mallet, C., Takahashi, E., and C. Dupuy, 2014, Tidal and seasonal effects on the consortium of bacteria, microphytobenthos and exopolymers in natural intertidal biofilms (Brouage, France), Aquatic Microbial Ecology92: 6-18.  

Pivato, M., Carniello, L., Moro, I., and P. D’Odorico, 2019, On the feedback between water turbidity and microphytobenthos growth in shallow tidal environments, Earth Surf. Proc. Land. 44(5): 1192-1206.

Ruddy, G., Turley, C.M., and T.E.R. Junes, 1998, Ecological interaction and sediment transport on an intertidal mudflqat I. Evidence for a biologically mediated sediment-water interface, In: Black, K.S., Paterson, D.M., and A. Cramp (Eds.), Sedimentary Processes in the Intertidal Zone, Geological Society, London, Special Publication 139: 135-148.

Smith, D.J., and G.J.C. Underwood, 2000, The production of extracellular carbohydrates by estuarine benthic diatoms: the effects of growth phase and light and dark treatment, Journal of Phycology 36(2): 321-333.

Underwood, G.J.C., 2002, Adaptations of tropical marine microphytobenthic assemblages along a gradient of light and nutrient availability in Suva Lagoon, Fiji, European Journal of Phycology 37(3): 449-462.  

Valentine, K., and G. Mariotti, 2014, Repeated erosion of cohesive sediments with biofilms, Advances in Geosciences39: 9-14.