General Comments:  The paper by Tang et al. uses an experimental marsh organ set up to examine the interaction of plant genotype (those adapted to flooding vs those unadapted) to flooding duration (daily, weekly, monthly). The authors hypothesized that flooding effects on microbial enzyme activity, decomposition, and community structure will be stronger in soils where the plant is not adapted to flooding than in systems where the plant is adapted to flooding. In general the paper is well written (though personally, I am not a fan of the extensive use of passive voice), the data are clear and well-presented and the results make an important contribution to the literature.  My primary concern with the results, as presented, is in the lack of description for tests of assumptions for the statistical analyses.  No data are presented on whether tests of assumptions were performed prior to ANOVAs, the the enzyme activity and decomposition variables, nor for the PERMANOVA.  in fact, the authors highlight the differences in the variability of the microbial community as a function of genotype, which technically violates the assumption of equal variances that underlies PERMANOVA analyses.  The conclusions fo the paper would be stronger if the authors documented the results for the tests of assumptions (e.g. levene’s test, betadisper, etc.) along with their statistical analyses.  Lastly, both in the abstract and the discussion, the authors continually refer to the effects of climate change on microbial activity/structure. I would recommend that the authors use caution with this broader construct. Their work was very specifically about flooding, not the myriad other affects of climate change. The authors argue that flooding/sea level rise is the most important climate change impact in coastal systems, which may be true, but this does not change the fact that there experiment was not a multifaceted climate change experiment, it was a single environmental factor x genotype experiment. Therefore conclusions such as “ adaptive genetic variation in plants can suppress or facilitate the effects of climate change on soil microbial communities” over-states what can be concluded from this work. I would recommend that the authors keep statements regarding the conclusions of this work firmly grounded in the effects of flooding, rather than the effects of climate change more broadly

Specific comments:

Line 49: this seems like an over-statement. There are several examples of work that has been done on linking plant infraspecific variability to C cycling, some of which was published by these authors (e.g. Mueller et al.).  I also find the “has not been done yet” argument to be less convincing than stating why it is important that the work be done. Perhaps switch this statement around to make it more clear why this study is needed and what knowledge gap it will fill rather than suggesting that there has been no work done on the topic.

Fig. 1: there is a decent amount of redundancy between the figure caption and the text, so if you are short on space you could edit this caption down.

Section 2.5: were tests of the assumptions underscoring these stats performed? This tests should be described in the methods and the results should be outlined in the results section.

Fig. 3: I find this figure to be really confusing, and it isn’t clear to me what it adds that cannot already be gleaned from Figure 2.  It isn’t exactly clear what is being compared - did the authors pick whichever max-min was largest from among the 4 enzymes or is this averaged across enzymes and averaged across flooding treatments? Perhaps it is because I wasn’t entirely clear on what the figure was showing, but it made it difficult for me to figure out what it added to the story.  I would think that the authors could remove it all together, or if they choose to keep it, it would be helpful to have more clarity around how they aggregated their data and what conclusion can be drawn (e.g. is it average EEA change across all flooding treatments, sum of all EEA changes?).

Line 260:  One of the assumptions of permanova is that variances are equivalent. This appears to violate that assumption and should be tested for using beta dispersion tests. This would support your assertion that the variability is higher in the unadapted genotypes, but it would mean the authors would need to rethink their permanova.

Line 266: the authors should be commended for not conflating the taxonomic composition of their microbial communities with what might occur in situ.

Discussion (first paragraph, principally) - I think the authors should keep the focus of their work on flooding, rather than climate change more broadly, as flooding was the only facet of climate change that was directly tested in this study.

The authors present a fascinating study that reveals compelling evidence of plant genotype mediating the influence of inundation on coastal marsh soil microbial communities. Overall, the work makes a strong contribution that substantively advances understanding of whether (and how) intraspecific variation in ecologically dominant plants influences key aspects of carbon cycling in coastal marshes, which disproportionately influence the global carbon budget. Accordingly, the work warrants publication as it will be of great interest to a broad audience, ranging from evolutionary biologists to soil biogeochemists. Before publication, the authors should make some relatively minor but important revisions that will strengthen the presentation of their work, as follows:

• Most importantly, the authors should not use terms such as ‘adaptation’, ‘adaptive’, etc. to describe functional differences in the two genotypes included in the study (and corresponding descriptions of the significance of plant intraspecific variation). These terms have very specific technical connotations, and their use requires evidence that phenotypic variation (i.e., functional variation) is (1) heritable; that the trait in question (2) responds to natural selection; and that responses in some way (3) relate to reproduction (i.e., fitness). The work presented here and elsewhere (i.e., Reents et al. 2021 https://doi.org/10.5194/bg-18-403-2021) does not present sufficient evidence that variation in tolerance to inundation is adaptive. Accordingly, the authors should substitute ‘tolerant’ and ‘intolerant’ (i.e., to inundation) to describe the two genotypes included in the study. Associated terms used elsewhere should be removed or replaced by technically suitable substitutes (e.g., the term ‘plant intraspecific adaptations’ should be replaced by ‘plant intraspecific variation’).
• From a methodological perspective, the source of the soil used for the experiment is somewhat concerning. It appears that the soil was not taken from the origin of either of the plant genotypes. This discrepancy should be noted as a caveat in the Discussion, as plant-microbe associations (and effects, outcomes thereof, etc.) can reflect provenance.
• From a statistical perspective, the number of correlation tests that were conducted is somewhat concerning. Further detail is warranted regarding the soil microbial parameters and plant biomass parameters that were examined. Also, depending on the number of tests conducted, significance should have been adjusted to account for multiple testing.

Below are notes that relate these comments to specific elements of the text as well as other notes intended to improve the presentation of the authors’ work.

SPECIFIC COMMENTS

ABSTRACT

L13. Topic sentence of the paragraph doesn’t align with the content of the paragraph. Revise. Possibly combine and abbreviate the first and second sentences in the paragraph to create a new, more representative topic sentence.

INTRODUCTION

L33. Change sentence structure to: “…It is therefore crucial to study the direct effects of climate change on soil microbial communities and resulting changes in ecosystem functioning. It is also important to examine plant-mediated, indirect effects (Bardgett et al., 2008; Van der Putten et al., 2013). Prior work on a wide range of ecosystems indicates that changes…”

L38. Change to “…on ecosystem C as well as greenhouse-gas and nutrient dynamics…”

L40. Topic sentence of the paragraph doesn’t align with the content of the paragraph. Revise. Possibly combine and abbreviate the first and second sentences in the paragraph to create a new, more representative topic sentence.

L57. Change to “These ecosystems are among the most effective…”

L67. Change to “The prevailing notion is that decomposition rates are inversely related to flooding.”

L69. Change to “have demonstrated”

L75. Change to “control of microbial C cycling in wetland soils by plant processes”

L76. Change to “yet largely overlooked”

L82. Change to “we hypothesized that”

L87. Change to “by intraspecific adaptive variation”

METHODS

L97. Change to “The experiment was conducted”

L104. Methods concern: one source of soil was used for the experiment. It also appears that the soil was not taken from the origin of either of the plant genotypes. This discrepancy should be noted as a caveat in the Discussion, as plant-microbe associations (and effects, etc.) can reflect provenance.

L111. Move “(n = 4)” to L109. Place after “four unplanted mesocosms”

L115. Provide more description here detailing (1) the extent of functional differences between the two genotypes (i.e., how different is the adaptive from the non-adaptive genotype, with regard to flood tolerance?). Also, provide a brief explanation of what was done to determine that the differences are (1) genetically-based, and (2) adaptive. It appears that sufficient work was done to demonstrate that the differences reflect heritable variation, but there isn’t evidence (yet) that the differences are adaptive. It is entirely possible that functional differences can reflect heritable, non-adaptive differentiation.

L172. How different were technical replicates with regard to community composition? i.e., what were the Bray-Curtis dissimilarity measures of replicates relative to other comparisons? This could be noted in the text or illustrated in a supplemental figure.

L175. What “soil microbial parameters and plant biomass parameters” were examined? Provide more detail here. Also, depending on the number of tests conducted, significance might need to be adjusted to account for multiple testing.

RESULTS

L220. The resolution of Figure 3 could be increased- the text appears a bit blurry.

L230-237. While this analysis was intended to be descriptive, the number of tests conducted warrants that significance be adjusted for multiple comparisons (i.e., Bonferonni corrections).

L240. Table 2. Presentation of significant correlations should be adjusted to reflect corrections accounting for multiple comparisons

L246. Correct typo. Should read “sensu Keuskamp et al., 2013))”

L256. Delete “the” before “microbial”

L262. Change to “soil microbial community structure”

L263. Delete “the” before “community”

L264. Change to “is shown”

L274-276. Long and complicated sentence structure. Trim it back by deleting “in ecosystems”

L286. Again, it might very well be that the functional differences among plant genotypes are not adaptive.

DISCUSSION AND CONCLUSIONS

L288. Topic sentence of the paragraph doesn’t align with the content of the paragraph. Revise. Possibly combine and abbreviate the first and second sentences in the paragraph to create a new, more representative topic sentence.

L298. How is genotype-induced variability in plant biomass different from genotype?

L321. Change to “…proven to be a powerful tool for characterizing…”

L327. Delete “parts of the”

L329. Reference to statistically significant correlations may have to be amended to account for concerns about multiple testing.

L335. Change sentence structure to “oxygen-deficient soils, like those found in coastal marshes. This suggests that it might be the most important mechanism, but strong genotype effects…”

L338-339. To support this premise, it would be good for the authors to refer to work done by Bernick et al. (MEPS 601:1-14 (2018)  -  DOI: https://doi.org/10.3354/meps12689) that illustrates heritable variation in nutrient acquisition among genotypes of a dominant plant (Spartina alterniflora) that engineers coastal marsh ecosystem attributes.

L353. As already noted, the use of the terms “adaptations” and “adaptive” are not well supported and should be replaced by terms like “variation” or simply not used.

L359. Delete “neither of which were part of the present investigation”