I have read “High capacity of integrated crop-pasture systems to preserve old stable carbon evaluated in a 60-year-old experiment.” The manuscript describes a study that models the POM and MAOM soil dynamics in continuous grain and rotational agricultural systems by combining long-term field SOC measurements with intermittent bulk sand respired soil CO2 radiocarbon data. The model indicated that SOC loss in the continuous grain system was primarily due to loss of MAOM, which was attributed to a higher outflow rate (decomposition) of the MAOM pool compared to the rotational system. The POM pool was also smaller in the continuous system, but proportional outflows (decomposition and transfer to MAOM) were similar to the rotational system. The authors conclude that the high C input into the POM pool in the rotational system maintains the MAOM pool, whereas the lower C input into the POM pool in the continuous system facilitates MAOM loss.

This manuscript is generally well-written, and the topic is of high interest. Long-term SOC datasets are very valuable, particularly when combined with radiocarbon data. To improve the manuscript, I have some comments that the authors may wish to consider.

General comments:

The introduction could be improved to better set up the ideas presented in the rest of the manuscript. Specifically, the concepts of POM and MAOM are not mentioned until the objectives at the end of the discussion, yet the POM and MAOM pool dynamics are the centerpiece of this manuscript. The concepts of POM and MAOM should thus be a central part of the introduction. In contrast, methodological details about radiocarbon (L61-63) and model specification (L73-78), which are tools used in the study, can be briefly summarized or omitted from the introduction and placed in the methods.

Several times throughout the discussion the authors mention that the difference between the rotational and continuous grain system is primarily caused by differences in C input quantity, not quality. However, the rotational system contains many legumes, which differ drastically in quality compared to grain. The authors surmise that litter quality is not important because the POM pools of both the rotational and continuous system had similar outflow proportions. Given that in this case litter quantity is confounded with litter quality, and that the model did not explicitly account for litter quality, it is very speculative to make statements about how litter quality affected the measured pools. I recommend that the authors reduce their speculations about this and in all cases make it clear that it is highly speculative and warrants more research.

A limitation of this study is that only the top 20 cm was measured and modeled, and the entire 20 cm was treated as a homogenous entity. Especially considering that these systems are now minimal or no-till, the top few centimeters of soil receive most of the aboveground inputs, and therefore they may be quite different than the soil below it. Moreover, root inputs are certainly present below 20 cm, but the model assumes that they are all within the top 20 cm. These limitations should be mentioned in the discussion.

An important caveat with the “crop-pasture rotational system” was that the pasture phase was not grazed or harvested. Instead, the pasture phase was mowed, and all biomass was allowed to return to the soil surface. While this does not detract from the mechanistic understanding gained from the research, it is important to specify that the results are likely a “best case scenario” in terms of C inputs and thus soil C storage. That is, if the pasture were a true agricultural system that was grazed or harvested for hay, then the total C inputs would likely have been much lower than the current mowed system. This should be mentioned in the discussion as to properly place the results into the context of realistic agricultural system management.

Some of the figures and tables seem to be redundant or supplemental in nature, while others could be improved clarity. More details are provided in the specific comments.

Specific comments:

L12-13: This would be a good place to qualify that these differences between pasture and continuous cropping systems (in this study and others) are mostly seen in surface soils (e.g., 0-20 or 0-30 cm).

L14-16: This would be more accurate if it read “We analyzed the temporal changes of 0-20 cm SOC stocks …”

L22-24: This sentence is somewhat unclear. To make the case that loss of MAOM-C was the important factor, it may be good to compare the age of pasture MAOM (~ 600 years) with the age of continuous crop MAOM (~ 200 years).

L30: Should “debate” be “discussion?”

L31-35: “On one hand/on the other hand” implies two contrasting statements, but these statements are not contrasting. Consider using different phrasing.

L31-33: Please provide a citation for this statement.

L44-45: It is a bit misleading and uninformative to suggest that “continuous monoculture” is “responsible for emissions of large amounts of C…” First, there is previous work to suggest that diversifying crops/rotations will likely only be effective at increasing SOC if the diversified system results in increased C inputs (King & Blesh 2017). Second, “continuous monoculture” describes a system rather than a mechanism; that is, it would be much more informative to list the mechanism by which a continuous monoculture could reduce SOC, for example, reduced inputs and increased tillage.

L44-55: These ideas are really the core of the manuscript, and I think this section warrants more length and detail. In particular, this is where POM and MAOM should be introduced as the manifestations of the “labile” and “stable” pools. There is also previous work in this area that can be explored here, such as King et al. (2020), Prairie et al. (2023), and references therein, that evaluate litter C input, quality, and SOC stabilization.

L45-47: Please provide a citation for this statement. Please also clarify whether these findings pertain to the entire soil profile, shallow depths, lower depths, etc.

L60-61: The 14C isotopic signature also reflects the 14C signature of the plant inputs.

L61-80: Radiocarbon and differential equation models are some of the tools used to study SOC (POM and MAOM) dynamics, but the SOC dynamics, not the tools, are the primary subject of this study. As such, I suggest only alluding to the tools in the introduction and then explaining them in more detail within the methods section.

L85: “Temporal changes” is a more explicit way to describe the “evolution.” I suggest removing “evolution” and replacing it with “temporal changes” or something similar.

L92-96: “Alternative hypotheses” implies that the hypotheses are mutually exclusive, but in this case, more than one hypothesis could be true. The “hypotheses” outlined are more akin to theories, where each theory could be false or true (null and alternative hypothesis, respectively). I suggest rewording this section to better describe these ideas.

L106: This states that “rainfall is highly variable among years, but it does not show a long-term trend (Fig. 1b),” yet Fig. 1b shows 3-month average rainfall, and thus neither of these points can be visualized in the graph. The graph should be changed to annual rainfall so that the reader can evaluate interannual variability and trends if that is the goal here.

L109-114: Figure 1 is ancillary in nature and therefore I suggest that it can be placed in supplemental information.

L123-124: Considering that this study only reports SOC dynamics to 20 cm deep, it seems unnecessary to report soil characteristics for deeper depths in Table 1. Moreover, most of the data presented in Table 1 are mostly ancillary and thus may not warrant inclusion in the main text. I suggest moving Table 1 to supplemental and summarizing some key components such as SOC, N, clay, and silt for the top 30 cm in the text on L120. E.g., “In 1985, a soil survey at the site reported SOC mass fraction of 20.8 g kg-1, N mass fraction of 1.7 g kg-1, 28.7% clay, and 63.7% silt (Table S1) for the 0-30 cm depth (Table S1).”

L135: Should “cropping sequence” be “crop rotation sequence?”

L139: It is unclear which treatments/rotation phases were tilled. In particular, did the grain phase of the rotational pastures receive tillage. Perhaps this could be explained in the next paragraph, around L151 and could be integrated into Figure 2.

L145-146: Is there a more descriptive phrase than “continuous agriculture” to describe the CC treatment? For example, a “continuous annual grain system?”

L150-151: For readers who may be unfamiliar with pastures, it may be worth noting here that three of the four pasture species are legumes, which are high in protein/N.

L156: While I understand the reasoning for mowing the pastures, the differences between a mowed pasture versus a grazed pasture should be noted here. Importantly, the amount of C returned to a mowed pasture is likely much higher than a grazed pasture, as the metabolism of the grazer would consume much of the C. Moreover, there are likely differences between plant vs. manure C inputs.

L159 (Fig. 2): It is unclear to me why the far-right boxes (end of the rotation) are colored beige and contain the same crop as the treatment at the far left (beginning of the rotation). Is this meant to imply that the rotation repeats? If so, I suggest simply writing the word “repeat” on the right side of the rotation, otherwise it suggests that there are two sequential years of the same crop (e.g., corn at the end of the rotation followed by corn to start the rotation).

L167: Please provide more details about how the soil was processed, for example sieving and drying. How were the SOC stocks calculated?

L173: Please provide more details about how the soil was prepared. Were they dried before incubations? Were the soils “pre-incubated” to avoid the CO2 flush from disturbance?

L189: Were these C values adjusted to the KrCr2O7 method values as was done with the LECO C values?

L201: I recommend replacing the term “global average” with term “overall average,” as “global average” could be misinterpreted as a worldwide average rather than am average within the dataset.

L203 (Table 2): The horizontal line between soybean and pastures can be removed.

L203 (Table 2): While it is necessary to use literature values to estimate total C inputs, the authors may wish to consider and discuss some of the shortcomings. In particular, using the shoot:root ratio presumably will give an estimate for total root inputs, but this study only focuses on the top 20 cm. In addition, for perennial species, the root system does not turn over every year, and therefore the root:shoot ratio will overestimate root inputs. A value of 0.5 yr-1 for relative root turnover would be more realistic (e.g., Gill & Jackson 2000), except in the third pasture year when pasture is replaced by grain crops, and thus the entire root system turns over.

L215 (Equation 1): Has this model been used previously (e.g., Spohn et al. 2023)? If so, please provide a citation for reference.

L216, elsewhere: The term “amount” is ambiguous. Presumably, this refers to the mass of C. Please use explicit terms such as “mass.”

L216, elsewhere: I believe that “k1 and k2” should be called “rate constants” rather than “rates.” In contrast, “rates” are the product of the pool sizes and rate constants (e.g., k2*Cs is the rate of loss from the Cs pool). Being correct and consistent with the language throughout the manuscript will help the reader follow through these concepts.

L221: Please list and define the variables used in Figure 3 within the figure legend (e.g., I = system C inputs, Cl = POM C storage, etc.).

L229: Is Fa mass fraction or atom fraction? Please be explicit for reproducibility purposes.

L234: Should this be listed as Eq. 3?

L234: Please explain what the “-25” after “sample” and “-19” after “OX” mean, or else omit them from the equation.

L246-247: Please give more details about how the priors were set. For example, was the prior normal or uniform?

L276: I think a title such as “Measured C dynamics” would be a better section title than “Measured data.”

L284: The phrase “Regarding the isotopic information” can be removed for brevity.

L296: The units for oxidation rate seem to be missing the basis. For example, is this mg C hr-1 g-1 soil or mg C hr-1 microcosm-1?

L297-298: This seems to be a repeat of the methods and does not need to be stated here.

L299: A reference to Table 5 may be appropriate here.

L310: “Once the parameterization procedure reached convergence (25000 iterations)” can be changed to “In the parameterized model” for brevity.

L318-319: The term “low” requires context, and the “% of outflow rate” needs to be defined. For example, “the transfer of POM to MAOM was small relative to the total POM outflow (i.e., MAOM transfers plus decomposition) …” It may also be helpful to indicate that this implies that most of the POM was being respired rather than becoming MOAM.

L320/309: Table 4 is redundant with Figure 4. Specifically, Table 4 is a summary of the information displayed in Figure 4. I recommend moving Table 4 to the supplemental, as the important information (means and distributions) can be seen in Figure 4.

L320 (Figure 4): It is difficult to compare the k2 and a parameters between R and CC treatments because the x-axes are not consistent. The inset diagram helps, but I still find it difficult to grasp when the x-axes are different. I suggest expanding the x-axes for the R treatment to match those of the CC treatment.

L330/335 (Figures 5 and 6): According to the methods, bulk soil samples were collected to a depth of 20 cm until 1996 and then were collected to a depth of 15 cm afterward. However, the SOC stock data presented here are all shown to a depth of 20 cm. Presumably, the measured 0-15 cm SOC stocks were extrapolated (e.g., multiplied by 20/15) to obtain an estimate for 0-20 cm stock. For transparency, please provide these details in the methods, and indicate this in the figure legend.

L330/335: These figures can be combined into one four-panel figure, as most readers will be interested in directly comparing the R and CC treatments.

L330/335: The colors used for bulk soil, MAOM, and POM should be consistent among panels.

L351 (Table 5): These terms should be defined in the table legend, particularly “stabilization flux” and “stabilization efficiency.” It may also be more intuitive to change the term from “release” to “output.” E.g., C input rate, total C output rate, POM C output rate, MAOM C output rate. The “stabilization flux” may be better termed “POM-to-MOAM transfer.”

L351 (Table 5): Perhaps this information would be better displayed graphically by making a figure similar to Figure 3, except there would be a panel for R and a panel for CC. The arrow widths could be proportional to flows and the box sizes could be proportional to stocks (Cl and Cs). This isn’t strictly necessary but would probably help users better understand the system differences.

L354: It would be ideal to define “age” and “transit time” here, even if they are defined in the methods, to remind the reader. I also recommend explaining what is meant by “system age.”

L355, elsewhere: This seems like too many significant figures, given that these results are based on a large data/model fusion, with significant uncertainty. For example, 545.65 ± 17.61 can probably be rounded to 546 ± 18.

L368: In panel 7d, can the authors explain why the mean transit times are disparate even though the density distributions look nearly identical? Is there something happening with the density distributions that we cannot see in the graph?

L385-387: This is a bit concerning, given that the model does not account for erosion. Moreover, even the comparison of SOC stocks through time assumes that there is no erosion. Is there any estimate for erosion rates at this site that could be presented here? I would think that erosion rates would be low, given that the slope is 3%, but it would be helpful to have a ballpark estimate.

L408-467: I think this discussion section would be clearer if the authors used language that clearly differentiated pool dynamics (i.e., Cl and Cs) versus flux dynamics (i.e., I, a, k1, k2). This would help the reader relate back to the underlying model (Fig. 3). For example, the R and CC system had a similar a and k1 flux constants, but the R system had approximately twice as much C input, which lead to the POM pool being 17% greater and the total flux of C from POM to MOAM to be greater. It would also be helpful to use different terminology when referring to rate constants (e.g., k1) versus rates or fluxes (e.g., (1-a)*k1*Cl).

L415-421: This seems somewhat contradictory. The first part states that litter quality is important, and the second part states that maybe litter quality did not matter. From this study, where litter quantity and quality were confounded, I think the conclusions are that 1) POM was greater in system with higher/better litter 2) modeled (not measured) POM flux dynamics (proportional transfer and decomposition) did not vary by system. However, since litter quality and quantity were confounded, and litter quality was not explicitly modeled, I do not think the model provides insight into whether litter quality impacted the pools and fluxes.

L430: Should “periods” be “treatments?” If not, please clarify this sentence.

L439-440, L452-453: This is an important point that may warrant additional attention, for example in the abstract. That is, even though POM contributed relatively little to the differences in SOC stocks, these model results suggest that having a relatively large POM pool is a prerequisite for forming and/or maintaining MOAM.

L442-445: While I agree with this explanation in principle, it seems like this would apply to both the R and CC systems. Are there other mechanisms that could explain why this was only seen in the CC system?

L460-461 vs. 466-467: These statements about litter quality again seem somewhat contradictory. The first states that the stabilization was not a function of litter quality, but the second states that stoichiometry (i.e., quality) could have an effect. Overall, these contrasting ideas should be rectified throughout the discussion.

L469: “Global Properties (Transit Time and Age)” can be changed to “C transit time and age.”

L483: The world “globally” can be removed to avoid confusion with “worldwide.”

L493-494: This sentence needs clarification. Specifically, it is unclear what is meant by “rejuvenation” effect. If anything, losing old MAOM seems like the opposite of rejuvenation.

L504-505: As the quality of litter was confounded with quantity, and quality was not explicitly modeled, the statement that litter quality was not important should not be a central conclusion.

References:

Gill RA, Jackson RB (2000) Global patterns of root turnover for terrestrial ecosystems. New Phytologist 147:13–31. https://doi.org/10.1046/j.1469-8137.2000.00681.x

King AE, Blesh J (2018) Crop rotations for increased soil carbon: perenniality as a guiding principle. Ecological Applications 28:249–261. https://doi.org/10.1002/eap.1648

King AE, Congreves KA, Deen B, et al (2020) Crop rotations differ in soil carbon stabilization efficiency, but the response to quality of structural plant inputs is ambiguous. Plant and Soil 457:207–224. https://doi.org/10.1007/s11104-020-04728-5

Prairie AM, King AE, Cotrufo MF (2023) Restoring particulate and mineral-associated organic carbon through regenerative agriculture. Proceedings of the National Academy of Sciences 120:e2217481120. https://doi.org/10.1073/pnas.2217481120

Spohn M, Braun S, Sierra CA (2023) Continuous decrease in soil organic matter despite increased plant productivity in an 80-years-old phosphorus-addition experiment. Commun Earth Environ 4:1–10. https://doi.org/10.1038/s43247-023-00915-1

The manuscript “High capacity of integrated crop-pasture systems to preserve old stable carbon evaluated in a 60-year-old experiment” is an interesting study of how different crop management practices can influence the carbon cycling in soils. The long-term nature of the study is unique and provides nice insight into these processes.

General comments:

The term "stable" is pretty loaded, I suggest the authors use a different term. Stability is being interchanged with decreased decomposition and with MAOM, which I don’t think is always true. From the model, the observed differences in 14C and C stock of bulk soil are likely due to higher decomposition rates in the CC system, which doesn’t necessarily indicate higher stability at the RR sites. I don’t think the authors have shown that the RR system C is more stable, just that the RR system increases C stocks by reducing losses. If the RR site were to be tilled in a similar manner to the CC system, would you expect the C stock value to persist, or would it decrease similar to the CC sites? If the latter, I don’t think it’s fair to say the C is stable, just that the land management decreases losses. The authors sort of get at this in lines 464-465.

Following this, I think it would be more appropriate to refer to the modeled pools as something like “fast cycling” and “slower cycling”, rather than calling them “POM/labile” and “MAOM/stable”. We know that some MAOM doesn’t persist for very long, so it is misleading to interchange the terms. Modifying word choice does not impact the conclusions of the model, which are quite interesting and provide nice perspective on SOC cycling rates in the two pools. (As an aside, it would be interesting to see the 14C of the POM and MAOM that the authors physically separated and how this matched up to the modeled pools, though I realize this may be outside the scope of this project).

Interpretation of the incubation data: I disagree with the statement that the incubation CO2 from the CC system is “more modern” than that of the R system (Lines 289-293). In the 0-10 cm,  the CC system incubation CO2 is -6.5 permil and the R is 9.13 permil, making the R system CO2 more modern. All of the other results are 14C modern (positive numbers falling on the bomb curve). You can’t distinguish which side of the curve they are on and therefore can’t claim one is more modern than the other.

Title: I suggest rewording this a bit following the above comments on wording

Technical/minor edits:

-Lines 31: Using the phrase “on the one hand” makes it sounds like the two perspectives are in opposition, but I don’t think these are.

-Line 117: should be “acidic”

-Line 146: clarify if fertilizer application was using in the crop-pasture rotation system

-Line 172: how many is “a large number”?

-Line 185: what was the actual temperature? (> 500 C)

-Line 229: The “a” in “Fa” should be subscript

-Lines 499 and 501: “Ancient” is a bit of a stretch for this age of carbon

-Lines 503-505: This sentence is speculative and not actually tested in the study.