The manuscript by Wang and co-authors on ‘Molecular-level carbon traits of fine roots: unveiling adaptation and decomposition under flooded conditions’ describes how soil changing soil oxic/anoxic conditions affect the molecular composition of a tree species naturally growing in changing water-logged/non-water logged systems, and highlights the species' adaptability of their chemical composition. The authors did not only compare roots from plants growing under different water/non-water logged conditions, they also used a combination of analytical methods (targeted GC-MS, non-targeted FTICR, as well as solid state NMR) to verify their applicability to grasp potential changes occurring at the chemical/compound specific composition. Moreover, they tested, whether the differences in root chemical composition also influenced their decomposability under different environmental conditions. The environmental conditions indeed changed the chemical root composition, with anoxic conditions leading to higher production/contents of polyphenolic compounds (with a high degree of unsaturation and aromaticity) and contained more non-structural compounds, and moreover, those roots decomposed faster.

The results of this study are very interesting and a good contribution for describing root traits beyond commonly measured parameter and show the adaptability traits. Moreover, the authors show that a combination of methods is needed to get a good coverage of non-structural carbon compounds in roots that could respond to changing environmental conditions. Overall, the manuscript clearly structured and well written. I would however clearly separate the technical question from the ecological question in the hypotheses section. The different methods that are now embedded as hypothesis i), but are in my opinion the tools to test the more ecological hypotheses ii and iii). I would suggest to turn the sequence at the end of the introduction around.

I appreciated the scheme in Figure 1, though it could be an idea to add, if known, some description of the expected C pool that could be extracted with the different fractionation steps. Was there an effect on root morphology detectable? Was there any effect on root N or other nutrient contents?

Moreover, there should be more detailed description of the statistics in the methods section, whether the data was tested or transformed for normality or homogeneity of variance or if non-parametric tests were applied. Another idea to show overlaps of compounds extracted with the different methods could be venn-diagrams for instance.

The results are clearly stated, I am just not sure why the authors decided to use ‘formulae’ and not ‘compounds’? I think that would be easier to understand and follow, if that was changed. Moreover, I would simplify and stick to C compounds or organic compounds and avoid carbonaceous. In the first section 3.1 of the results there could be also some statistical tests added (or point to a Table with statistical results testing the different fraction distributions).

More detailed comments:

Line 12: carbonaceous organics is a bit counterintuitive – the definition of organic is that they should contain C, while carbonaceous suggests rather inorganic C sources..

Line 16: what was the hypothesis or expectation how different environmental (oxic – anoxic) should cause in roots? Why were those two extraction methods selected to get different fractions?

How were the decomposers selected? Was this maybe also a result of communities present under oxic conditions vs. anoxia?

Line 29: check reference, it should be McCormack 2015

Line 30: what other underground organs do plants use?

Line 30: delete the comma after ‘and’

Line 34: I think it should be C containing organic compounds (but could be just organic compounds (as per definition they should contain C). and maybe already give examples from the start of the MS).

Line 35: See e.g. the reviews by Freschet, which could be of interest to the authors: doi:10.1111/nph.17572, or  doi:10.1111/nph.17072

Line 37: ancestry meaning ‘phylogenetically conserved’?

Line 50: not sure if this should be a technical paper?

Line 60: do some plant species adapted to water saturated situations have undergone trough a selection towards different compounds?

Line 83: this is not a real hypotheses, but a technical question?

Line 93: I think this is very important information that there are many plants growing at the waterline, this has not totally come across in the introduction. It sounded like a greenhouse experiment so far.

Line 99: based on the previous studies, what should be the main components extracted in each fraction that would need such a highly work- and chemical intense fractionation scheme? It might be nice to add what is known what compounds the different fraction are supposed to contain.

Line 105: derivatized.

Line 150: It would be great if the statistical section could be extended. Were all data normal distributed, were data transformed if they were not?

Line 156: based on the figure 2a it looks as if the  FKOHy and CuOCX fraction are very similar both in sized and C content. Would be great if there is some statistical support to detect if they are similar or different.

Line 158: give exact numbers here for the residual biomass after all digestion steps, and moreover, test also if there were differences between the WGR and SGR.

Figure 4: please give a clear description of the y-axis – in the text it is referred to C here to OC

Line 214: and/or

Line 218: what is meant with the common formulae? Common compounds? assignable compounds? classified compounds?

Figure 5 it is difficult to see if the treatments/categories overlap, it would help to reduce the transparency of the dots.

Line 266: change to targeted and non-targeted approaches

Line 280: were there changes in N content or other micronutrients observed? In certain environments those can be important for decomposers and decomposition rates?

Line 286: Does less ash indicate more organic compounds being lost during ignition, right? Why is this in contrast to the previous sentence?

Line 291: but the compounds are specific to different stressors: e.g. suberin has several times been reported to be increased in response to water stress see e.g. doi: 10.3390/metabo11110735

Line 309: one could also suggest that in soil plant roots need more and stronger structures supporting a lot of lignin-phenolics, to endure the more harsh conditions.

Line 320: it would be great if a sentence about potential differences and impacts on decomposer communities could be discussed see e.g.  https://doi.org/10.1016/j.soilbio.2020.10779 as well as the conditions for those decomposers.

Line 343: , ‘counteracting’ the reducing effect .. or ‘and counteract’

Comments:

The manuscript entitled “Molecular-level carbon traits of fine roots: unveiling adaptation and decomposition under flooded condition” focused on the differences of chemical traits of soil-grown and water-grown fine roots of a tropical tree. The authors extracted compounds in root samples and charactered the chemical compositions using targeted and non-targeted analysis techniques. Targeted analyses such as GC-MS can provide more accurate information of chemical compositions (e.g., specific compounds), but may also lose many information since a lot of compounds cannot be identified using this method. I am glad to see that state-of-the-art analyses were used in root studies, which should advance mechanistic understanding of root acclimation and associated biogeochemical processes under changing environments. This study shouldh should raise broad interests to the readers at SBB.

       Overall, this manuscript is well written with sufficient data to support the main findings. The experiments are also well designed. It is amazing to see that a single tree has different habitats for the growth of roots in natural conditions. Similar studies may need to design split-root systems. I am really enjoyed reading through the manuscript, although I still have some minor comments.

Specific comments:

Line 15-18: This sentence is too long, please split it into short ones.

Line 24-25: Is it necessary to emphasize the techniques as a highlight at the end of the abstract. I do think more emphasizes should be on the research question per see, although combination of diverse techniques contributed to the findings.

Line 29-31: long sentence.

Line 31: the fine-root tissue chemistry

Line 81-83: Is the first hypothesis necessary? As commented above, this is not a methodological paper to me, although I understand you also want to test the feasibility by combining different analytical methods. Otherwise, you can test it using any experimental systems, but why focusing on the flooded vs. the non-flooded condition?  I suggest removing this hypothesis since the data you provided can show the validation.

Line 150-152: please elaborate the statistical analysis further. This section is too simply described in current version.

Line 323: delete ‘to say’.

Line 320: it is a little bit weird to me to see the discussion of hypothesis three in the section of ecological implications. Why not move this part of discussion in a separated section? Or is the subtitle of ecological implication necessary here? When talking about ecological implication, we typically put it into a broader scenario, rather than discussing a part of main results at this stage.

Line 344-347: Okay, when reading to the very end, ‘Together, …’, it sounds like all these results are just for validating the complementary information by combining GC-MS and FT-ICR MS analyses? If this is the case, please reconsider my previous comments about this concern. If not, please rephrase the last sentence in the conclusion and consider my suggestion above, which may cause confusion to readers.