Review comments for Razanamahandry et al., 2024

This is an interesting article that tackles an important but understudied topic, namely the role of (tropical) lakes in modulating inland water carbon fluxes. I’m glad to see the focus on carbon sources and fluxes upstream and downstream of the lake. There is a huge wealth of data contained in the paper, and for the most parts the authors do a solid job of analyzing these data coherently. Ultimately I think it will be a valuable contribution.

However, there are a number of issues that need to be addressed before this should be published in Biogeosciences. I would characterize these as major revisions. I summarize major issues below, and then provide line by line comments.

Peter Douglas

Introduction: I found the introduction to be somewhat unfocused, and a clear rationale for the study does not emerge. I think the authors should put more attention to the importance of this study in a global context, and how this site is representative of globally important ecosystems. What questions in global carbon cycling and inland water carbon fluxes does this study help us address? The discussion of environmental impacts of sediment from soil erosion is interesting, but given the topic of this study it seems the introduction should be more focused on carbon cycling. Also, it seems part of the expressed motivation of the study is to interpret paleo-proxy data, which I think is tangential. Again I think these data are more interesting in terms of modern day carbon cycling and that should be a larger focus. See cited paper Cole et al., 2007 and Regnier et al., 2020 for examples of key questions in inland water carbon cycling.

Regnier, Pierre, et al. "The land-to-ocean loops of the global carbon cycle." Nature 603.7901 (2022): 401-410.

Sampling Design: I think the selection of sampling sites and the sampling design needs more clarification and elaboration. How were inflowing rivers chosen and why were some sites sampled at a higher frequency? How were the lake sampling sites chosen, and importantly what depth was water sampled from? Lake sampling is not really described at all. How far downstream of the lake outlet was the outflowing river sampled? It seems to me the marsh sampling should be discussed in the same section as the water sampling, or at least before the analytical methods. Why were only marsh plants sampled and not terrestrial plants or phytoplankton, which are also probably important OM sources? The point of the cores from the marshes is not that clear- maybe explain a bit more the rationale for collecting cores as opposed to surface samples, and what information is provided by the depth profiles.

Analytical Methods: This section is very dense and hard to follow. I would suggest splitting into subsections if journal allows. Some reorganization is needed. PCO2 measurements should proceed the estimates of DIC concentration since they are used for that. There is no mention at all of the CH4 measurements that are presented, which is a major oversight.

Results: This section is very dense and hard to follow. If possible to break into subsections that would make reading easier.

Vegetation data: As mentioned above, having d13C values of local terrestrial plants and phytoplankton, or at least estimates, would really be helpful and complement the data shown in Table 3. The 13C values of subsoils are referenced but the actual numerical values should be summarized, and it is unclear why topsoils are not included. In line 448 there is discussion of a mixing model based on plant isotopic values, but this is quite unclear and hard to follow. More details are needed, and the relative abundance of different plant types should be specified, ideally in a table.

Phytoplankton 13C calculation: I’m afraid this is a gross oversimplification. This fractionation factor can very hugely and is sensitive to biological and environmental variables like growth rate and light, as well as differences between taxa. Use of a single value of 20‰ is too simplistic, and based on my quick review is on the high end, as opposed to an average value. So I don’t think this is appropriate. In addition the uncertainty in this estimate needs to be accounted for. There is an extensive literature on this, but see for example:

Burkhardt, Steffen, Ulf Riebesell, and Ingrid Zondervan. "Effects of growth rate, CO2 concentration, and cell size on the stable carbon isotope fractionation in marine phytoplankton." Geochimica et Cosmochimica Acta 63.22 (1999): 3729-3741.

De Kluijver, A., Schoon, P. L., Downing, J. A., Schouten, S., & Middelburg, J. J. (2014). Stable carbon isotope biogeochemistry of lakes along a trophic gradient. Biogeosciences, 11(22), 6265-6276.

The Fry et al citation is quite outdated. Including more uncertainty in this calculation is required, and likely has effects on the inferred contribution of phytoplankton.

Consideration of hydrodynamic processes: Differences in %POC between the TSM and soils was suggested to indicate a different, more organic rich source. However, this could also reflect sorting and selective settling of eroded soil that could lead to greater %POC in the lake. For example, soil minerals may selectively settle and deposit in sediments, whereas OM rich material may be more likely to be suspended. I think this is worth consideration. This could also potentially explain the higher %POC in the lake vs the inflowing rivers.

More detailed implications: I think it would be really valuable to see a bit more discussion of the implications of this work at the end of the discussion. What does this mean for the role of lakes in riverine carbon transport and emissions? Does the presence of lakes in (tropical) rivers lead to a net increase or decrease in emissions, and does it change the overall source of C that is being respired? Do your results have implications for the carbon cycle effects of current anthropogenic changes in the catchment and the lake? Will greater erosion and/or rice production lead to changes in the GHG fluxes from this system or the downstream export of carbon? I think addressing some of these questions will enhance the impact of the paper.

Line by line comments:

Line 38: this phrase about degassing is not clear to me.

L61: This sentence is not clear. If the C fixed is not buried or emitted where does it go? Exported as DOC downstream?

L70: Be more clear why data from Madagascar is valuable in a global sense.

L90: Specify how the wetlands have been altered.

L105: This is an important point and isn’t totally clear here. Based on the Broothaerts paper there is a huge amount of sedimentation in the floodplain (100x greater than the lake) and a lot in the wetland (10x greater than the lake), leading to very low sedimentation in the lake itself.

L130: This sentence is redundant with the earlier part of the paragraph.

Figure 2: Is it possible to add how this hydrological difference affects lake level?

L176: Awkward phrasing- try to rewrite.

L195: Much more details on lake sampling needed.

L298: There is not really much on d15N in the paper. Was it used at all? I recognize the authors are providing a wide range of data that was not used in the paper. Perhaps methods for these analyses should be in a supplement so that they can be used later but do not distract in the main text.

Figure 6: The cause of the gaps in data are not clear to me, make clearer here or in the methods.

L358: It is interesting that %POC is lower in the outflow than the lake. What is the source of inorganic TSM in the outflow?

Figure 9: Is any information on the age-depth relationships in the cores available. The core data in general is not that informative, so maybe it could be more simply summarized as a source of OM.

L454: Give numerical values (i.e. average plus standard deviation) for the lakes in East Africa being compared to.

L469: In addition to the issues discussed above, if there is high C fixation this can lead to enrichment of d13C in the water column (i.e. a Rayleigh distillation effect) and potentially lead to erroneous estimates based on the fractionation factor.

See for example: Van Dam, Bryce R., et al. "CO2 limited conditions favor cyanobacteria in a hypereutrophic lake: an empirical and theoretical stable isotope study." Limnology and Oceanography 63.4 (2018): 1643-1659.

L474: This begs the question: are the differences between the inflow water and the lake/outflow water significant?

L513: Again, provide numerical values for these other lakes.

L517: Need a citation for these data from the  Congo.

L524: I think a more detailed explanation for the connectivity causing high pCO2 and pCH4 is needed.

General comments:

This study investigates the carbon biogeochemistry of Lake Alaotra, Madagascar, by analyzing variations in carbon pools, CO₂, CH₄, and other parameters over a complete hydrological cycle. It offers valuable and much-needed data that contribute to advancing discussions on the role of tropical lakes as “biogeochemical reactors.” While the authors have made an important effort to underpin their discussion, I believe that some broad generalizations weaken certain key findings of the research. Therefore, I believe this manuscript should undergo major revision or be resubmitted before publication.

The introduction offers extensive details about the study area but lacks sufficient emphasis on the main research objectives, making it difficult to fully understand the rationale of the study. The authors should reconsider the level of attention given to ‘lavakas’ (l12, l83–l86, l124) and paleoenvironmental interpretations (l108–112), as these topics are not directly connected to their main findings. Additionally, the manuscript would benefit from clarifying the gaps in the carbon cycle that this research aims to address, providing a stronger rationale for the study.

The authors mention a “selection of rivers,” but the criteria for choosing these two rivers and their representativeness regarding the overall water balance of Lake Alaotra are not clearly explained. Additionally, highlighting these rivers on the map in Figure 1 would improve visualization. There is also some ambiguity about how many rivers were sampled during the high- and low-water field trips. Overall, the sampling scheme and the methodologies used are somewhat unclear and lack key details. For example, what were the water depths at the sampling sites? How were the sampling points in the lake selected? While coordinates are provided in the Supplementary Data, important implications regarding the sampling strategy should be discussed in the main text. For instance, CH₄ concentrations in lakes can vary significantly depending on proximity to the margins. Addressing these aspects would greatly enhance the study.

The results section would be much more reader-friendly with the inclusion of additional graphs and tables. Biplots, in particular, could greatly aid in comparing the ranges of organic carbon across soil, lake, and river samples. In the discussion, although the evidence suggesting that the increase in %POC in the lake is likely driven by phytoplankton input is relatively solid, the text is structured in a way that makes the argument somewhat unclear. A clearer and more focused presentation of this idea would improve the coherence of the discussion. Also, the authors may get interesting perspectives on erosional patterns by delving deeper into the TSM changes.

My main concern, however, lies in section 4.2. It is important to emphasize that the separation between POC and DOC fractions, based on size, represents an “instrumentalist” approach that overlooks key factors. Most importantly, a primary control on %POC and TSM, the energy of the environment, was severely neglected in the discussion. This, naturally, has significant implications for some of the interpretations. Similarly, degradation, which is also size-dependent, probably play a critical role in shaping the OM δ13C signatures observed in the system but was not adequately addressed. Additionally, although the conclusion that DOC and POC sources are uncoupled is reasonable, the entire discussion regarding DOC sources seems to oversimplify the system and is not fully supported by the data presented in the article.

Lastly, it would be great if the authors could place the obtained results within a broader regional context, highlighting their implications for the current understanding of the tropical carbon biogeochemistry cycle.

Specific comments:

L12-14: As I read these lines, I thought the main focus of the article to be different. Consider focusing the beginning of the abstract towards the main target of this article.

L26: Not necessarily ‘surprising’

L31: I'm not sure if "was expected" is the right expression here. Do you mean "was found," as in: "δ13C data indicated that marsh vegetation was the main source of net DOC inputs, while phytoplankton likely contributed to POC in the lacustrine waters."?

L100: I recognize that this study is present in the literature, but its conclusions don't seem well-supported by the findings. I'm not sure if continuing to reference it truly benefits the advancement of science.

L108-L112: I am not sure how this directly relates to the main subject of the article.

Figure 1: Please consider highlighting which rivers were measured monthly and which were not measured during the dry season.

Figure 9: Are there any considerations regarding changes in the parameters for different depths that can contribute to your discussion?