Reviewer 1

We thank the reviewer for the positive feedback.

We agree with the reviewer that wetting and drying cycles may cause anaerobic or anoxic conditions. However, in this experiment, the soils were kept wet at field capacity only for 24 hr and then left in open air for moisture loss (to initiate drying conditions) and the soils were packed to a height of 3-5 cm in jars with 12 cm width. Hence, we do not believe our experimental conditions have anoxia in the soil. Indeed, we have not measured a decrease in nitrate in our soil solution samples (which would happen if conditions were anoxic). We can include graphs if considered necessary to show this). The organic amendments except anionic polyacrylamide (PAM) were used in dried form to overcome differences in moisture content and particle sizes. While there may have been some losses of nutrients in the organic amendments due to drying, the nutrient content was measured on the dry material. Hence, we do not believe this would affect the interpretation of our results.

We also agree that different microbial communities may be added (or favoured) by adding organic amendments. However, the focus of our paper was not on different microbial populations but on aggregation (by whatever means the aggregates are formed, be it different microbes or iron oxides). While we measured the soluble chemical fractions (soil solution composition) in our samples (these data are reported in the supplementary section of our paper), we have not analysed if there are changes in the mineral phases during the trial since this was outside the scope of our experiment. 

The focus of this experiment was to understand the effect of wetting and drying cycles on improving the structure of sodic soils under the application of different organic amendments. Therefore, to correlate the changes in aggregate stability and aggregation with microbial activity, daily microbial respiration was measured. In our earlier study (Niaz et al 2022) we measured Dissolved Organic Carbon (DOC) using the same soils and amendments under continuous wet conditions and found that DOC and soil microbial respiration were strongly positively correlated with each other, hence we are confident relating microbial respiration to DOC in this paper.

Reviewer 2

We appreciate the time and effort the reviewer spent on our paper and for the constructive criticism. We trust that our revisions are satisfactory.

The characterization of microbial activity was only based on microbial respiration since we analysed the changes in dissolved organic carbon using the same soils and same organic amendments under continuous wet conditions in our earlier paper which is now published (Niaz et al 2022). The results showed that dissolved organic carbon is strongly positively correlated with microbial respiration. Likewise, the chemical characterisation of the organic amendments used in this study is published in Niaz et al., 2022 (https://doi.org/10.1016/j.geoderma.2022.116047).  We agree with the reviewer that a detailed study of the microbial population can be performed, but this was outside the scope of this paper.

1. We have clarified the hypothesis as follows: “We hypothesised that i) organic amendments will increase the microbial respiration and improves the formation of large macroaggregates and MWD, (ii) gypsum will improve aggregate stability due to increases Ca concentration and ionic strength, iii) organic amendments act synergistically with gypsum on aggregation, and iv) repeated WD cycles will increase the process of aggregate formation and stability”.
2. We have revised the results section as suggested by this and other reviewers.

Line comments

1. Organic matter in title has been replaced with organic amendments. The title has been updated as “Wetting and drying cycles, organic amendments and gypsum play a key role in structure formation and stability of sodic Vertisols”
2. The full form of PAM has now been incorporated as “In contrast, dispersion was significantly reduced when soils were treated with chicken manure, whilst anionic polyacrylamide only had a transient effect on aggregate stability”.
3. The four organic amendments were chosen because of two reasons: 1) they were easily available and are being used by farmers, 2) LP is used as green manure and studies have shown it is effective in ameliorating sodic soils, and 3) PAM is used in mining and construction to treat sodic dispersive soils. Furthermore, these amendments were different in terms of their chemical properties (Table 2) and C functional groups (Niaz et al., 2022) and may give a good contrast between the amendments.
4. The 0-10 cm soil layer was chosen because topsoil has the greatest OM content and microbial activity. In any case, Vertisols are relatively uniform in texture and structure throughout the soil profile; using subsoil would not add much information to the study.
5. The soil was sieved to 10 mm as we wanted minimise physical disturbance of the natural soil structure. The soil contained no stones or coarse fragments, and the visible plant litter was manually removed.
6. The experiment was performed jars with 12 cm diameter and 15 cm height, and the soil was packed to a height of 3-5 cm (depending on the bulkiness of the organic amendments).
7. As there were 10 treatments, individual error bars or asterisks would have cluttered the graphs. Therefore, we preferred to insert the Tukey HSD bar in graphs.
8. The discussion has been revised as follows “the results of this experiment showed that addition of gypsum (Ca) significantly reduced soil dispersion and increased aggregate stability. This improvement in aggregate stability is because of the increased EC (ionic strength, Fig. S4) and decreased SAR (Fig. S5) after the addition of gypsum. The increased EC likely resulted in the flocculation of soil particles by reducing the diffuse double layer (van Olphen 1977, Ghosh et al., 2010, Bennett et al. 2015). Improved stability was also observed when organic amendments were applied with gypsum especially in G+PAM, G+LP, and G+FLM treated soils, which when applied alone were not able to improve aggregate stability. The PAM had an initial positive effect but led to decreased stability at completion of the second WD cycle. Although, the addition of gypsum increased aggregate stability, it was observed that addition of gypsum did not affect the proportion of large macroaggregates and MWD. However, when organic amendments were added with gypsum an improvement in proportion of large macroaggregates and MWD was observed in G+LP treated soils. This can be explained as Ca-bridging effect through which clay particles are attached to organic matter and polyvalent cations resulting in the formation of macro and micro aggregates (Wuddivira and Camps‐Roach 2007).”
9. More references highlighted in blue italic colour have been included as “Although the maximum respiration rate was observed during the first WD cycle for LP and G+LP, the proportion of large macroaggregates and MWD increased at the end of fourth WD cycle. However, the proportion of large macroaggregates did not increase much as compared to the first WD cycle, likely because microbial activity was lower (Cosentino et al. 2006; Zhang et al. 2022). One of the possible reasons of increased MWD could be the accumulation of microbial binding agents over time that released continuously from microbial activity due to organic matter decomposition (Rahman et al. 2018).
10. The conclusions are revised as “The stability of dispersive sodic Vertisols was improved by the application of organic amendments and gypsum, which was further enhanced by alternate WD cycles. Gypsum reduced soil dispersion but did not affect the proportion of large macroaggregates and MWD. We observed that not all organic amendments were equally beneficial in improving soil aggregation and aggregate stability. LP significantly increased the proportion of large macroaggregates compared to FLM and PAM. In contrast, CM significantly reduced soil dispersion as it had higher calcium content. It was also found that PAM only had a transient effect in controlling dispersion. In the absence of organic amendments, repeated WD cycles reduced the dispersion of sodic soils, but when organic amendments were added (with or without gypsum) soil aggregation and soil stability was improved even more. It is likely that soil microbial activity contributed to the aggregate formation. Implementation of these findings in the field would favour the use of organic amendments with gypsum to improve the physicochemical properties of sodic soils, which is further enhanced by WD cycles. The aim should be initially to prevent soil dispersion which can be achieved by the application of Ca (through application of gypsum) and then to build larger aggregates which can be achieved by the application of organic amendments”.

Reviewer 3

We are thankful to the reviewer for the critical and positive feedback.

1. We agree that a correlation does not prove the existence of a mechanism or cause. We represented the correlations among different soil physical, chemical, and microbial characteristics as PCA biplots after each WD cycle to show how soil properties change with repeated WD cycles. We have reworded the main text making it clearer that we refer to correlations only.
2. We have added more references to place our findings in a broader context and relating our results to other work done with Vertisols (Ghosh et al., 2010, Rahman et al., 2017, Rahman et al., 2018, Bennett et al., 2015, Nachimuthu et al., 2022).
3. The hypotheses have been updated as shown for reviewer 2.
4. The introduction have been revised by adding information about soil microbial respiration and aggregate formation as “Although, several researchers have reported that the addition of organic materials causes a rapid stimulation of microflora, which increases soil microbial respiration, in response to which extracellular polysaccharides are produced that helps in the formation of soil aggregates (Bossuyt et al., 2001), but the studies investigating the effect of organic amendments in improving the soil structure are inconclusive. For instance, the extracellular polysaccharides and large polyanions can bind clay particles into stable macroaggregates. On the other hand, organic anions can enhance dispersion by increasing the negative charge on clay particles and by complexing calcium with other polyvalent cations (such as those of aluminium), hence reducing their activity in soil solution (Ghosh et al. 2010)”.
5. We have revised sections 3.1 and 4.1 to make our statements clearer. For example, the reviewer has highlighted a sentence in line 402 “the proportion of small macroaggregates did not increase after the second WD cycle”, which was changed to “at the completion of the second WD cycle”. (Samples were collected for aggregate size analysis after completion of either 1, 2 or 4 WD cycles). In our revision we will explain the data in more detail and then speculate about the reasons – for example we have included a Figure reference in the text: “The WD cycles result in rearrangement of pores and soil particles and may lead to increased rigidity and stability of soil aggregates (Horn et al. 2014). We observed a marked change in aggregate size distribution with repeated WD cycles (Fig. 1), from macroaggregates (large macroaggregates and small macroaggregates) at completion of the first WD cycle, to microaggregates at completion of the second WD cycle, and back to macroaggregates (large macroaggregates and small macroaggregates) at the fourth WD cycle. We suggest that extracellular polysaccharides formed by microbial activity (soil microbial respiration, Fig. 3) are responsible for the formation of large macroaggregates at the first WD cycle. At the second WD cycle, the microbial activity greatly decreased (Fig. 3) and macroaggregates (large macroaggregates and small macroaggregates) were broken down into microaggregates and silt+clay”
6. The reviewer showed concern about the statement we made about the breakdown of large macroaggregates compared to microaggregates during WD cycles. We will rephrase that sentence as “macroaggregates are more susceptible to disintegration during wet sieving compared to microaggregates at the completion of second WD cycle. By the fourth WD cycle, some rearrangements of soil particles likely occurred, facilitated by soil drying, thereby rebuilding macroaggregates.” We could also insert a schematic to illustrate the process.
7. The conclusions have been revised as shown for reviewer 2.
8. The new citations have now been included at various points in manuscript some of which are Brangari et al., 2022, Freser et al., 2016, Zhang et al., 2022.
9. The previously unpublished data has now been published and available online as Niaz et al., 2022. (https://doi.org/10.1016/j.geoderma.2022.116047)
10. All the small corrections have been incorporated in the manuscript and the legend to Fig 2 has been inserted.

Reviewer 4

We thank the reviewer for their time and constructive feedback which helped us to improve our paper.

1. The introduction is revised as already suggested by other reviewers. In addition, the reviewer asked to add a brief information about how gypsum and organic amendments can affect aggregation and aggregate stability which has now been incorporated in the main text. An overall brief explanation about sodic soils and their poor structure is given in the introduction from lines 52-69. The effect of organic amendments or organic matter on aggregate stability was briefly described in introduction in lines 84-86. However, the role of gypsum was not explained which has now been added in the introduction as “Traditionally the management practices used to improve the structure of sodic soils involves the displacement of Na ions from the soil exchange complex with the help of divalent cations such as Ca or increasing the ionic strength of soil solution (Ghosh et al. 2010), both of which can be achieved by the application of gypsum to these soils. The effect of gypsum for increasing ionic strength is immediate, but short lived. In contrast, the effect of gypsum for providing the counter ion (Ca to replace Na) is permanent unless additional Na is added to system (e.g., using poor quality irrigation water)”.
2. The aims have been rewritten as “Thus, in the present study we used two sodic Vertisols, with the aim to: i) determine the role of gypsum and different organic amendments on aggregate formation and stability, ii) explore the combined effect of gypsum and organic amendments on soil physico-chemical and microbial properties, iii) investigate the effect of WD cycles on microbial respiration, iv) assess the effects of WD cycles on aggregate formation and stability, and v) determine how many WD cycles are needed to improve aggregate stability.
3. The hypothesis has been rewritten as shown for reviewer 2.
4. We have use two-way ANOVA to analyse the results which makes the description of results rather complex and repetitive. That’s why the discussion was written as the relative role of each factor (WD cycles and organic amendments or gypsum). The interaction of these factors was clearly demonstrated by presenting PCA biplots after first, second and fourth WD cycle in Fig. 5 and section 3.4 (lines 341-356). The two-way ANOVA table can be included in the supplementary data.
5. The dose of PAM in Table 3 has been corrected.
6. The discussions have been revised as suggested by other reviewers (see reviewer 2).

Reviewer 5

We thank the reviewer for the positive feedback and hope our changes are satisfactory.

1. The aims and research hypothesis have been revised as recommended by other reviewers.
2. The sentences are reformulated to make it clear for readers to understand the changes driven by different amendments or WD cycles.
3. The information regarding Vertisols has been incorporated in introduction as “Apart from the changes in soil structure due to the addition of different ameliorants, WD cycles can lead to more intensive changes in structure of soils dominated with smectitic clays (Vertisols). The WD cycles can directly affect aggregation of these soils through physical processes (Utomo and Dexter 1982; Denef et al. 2001). These soils are generally characterised as self-mulching soils as they exhibit shrink-swell properties imposed by the WD cycles (Pal et al. 2012). Vertisols cover a total of an estimated 340 million ha in the world (Australia, Asia, Africa, and America), out of which approximately 150 million ha is potential crop land. However, the physical properties and moisture regime of Vertisols represents serious management constraints (Pal et al. 2012). Sodic Vertisols are common in arid parts of the world. The effect of sodicity on the physical properties of Vertisols is still a subject of debate”
4. We are not sure we correctly understand the question about preincubation; soils were not pre-incubated in the study, but they were collected in the field and would be pre-incubated there. We are not sure why pre-incubation would be useful – in the field, treatments are applied without pre-incubation. Our apologies if we misunderstood the question.
5. The effect of rapid slaking was not checked as the soils were subjected to end over end shaking for the measurement of easily dispersible silt+clay.
6. The conclusions have been revised as suggested by other reviewers.

Minor corrections

1. Line 113 revised as suggested by reviewer
2. Line119 corrected as suggested
3. The formula used for gypsum requirement has now been incorporated in the main text from line 175 -176 “The gypsum requirement of both soil samples was calculated based on the formula given by Oster and Jayawardane (1998) as follows:

Gypsum requirement (GR)= 0.00086 x F x D x ∂_b x (CEC) x (ESP_i-ESP_f)

Where F is exchanged efficiency of Ca-Na and for this case considered equal to 1.

D_s is the depth of soil to be reclaimed (cm)

∂_b is soil bulk density (g/cm³)

CEC is cation exchange capacity (cmol⁺/Kg)

ESP_i is initial soil exchangeable sodium percentage

ESP_f is final or desired exchangeable sodium percentage.

Hence for soil 1 GR= 0.00086x1x10x1.29 (23) (14.9-6) = 2.27 Mg/ha

And for soil 2 GR= 0.00086x1x10x 1.29 (24) (15.9-6) = 2.52 Mg/ha

As an approximation, a single rate of application of gypsum, 2.5 Mg/ha was selected for both soils.

Reviewer 6

We are highly appreciative of the feedback given by the reviewer.

1. The full form of PAM has now been incorporated in main text in line 28.
2. Abbreviations have now been spelled out in the Introduction and Materials and methods
3. The hypotheses have been revised as recommended by other reviewers.
4. We presented Table 1 and 2 after the description of soils and organic amendments in the Materials and methods section, but we don’t mind to move the tables to the Results section is the editor recommends.
5. As explained for reviewer 2, we prefer to use the Tukey’s HSD bar to avoid cluttering the graphs.
6. The unpublished data at that time was under review and now has been published as Niaz et al., 2022 (https://doi.org/10.1016/j.geoderma.2022.116047).

Specific comments

1. As explained for reviewer 2, topsoil layer has high OM and microbial activity and Vertisols are relatively uniform in texture and structure to depth
2. Three core samples were collected for the measurement of bulk density for each site (Soil1 and Soil 2) while the bulk soil samples were collected with a shovel to 10 cm depth.
3. The formula used for gypsum requirement has now been added in materials and methods section as advised by reviewer 5.
4. Our apologies but we do not understand what is meant by “Amend “change” ”
5. The significance for each parameter is indicated in the text and figures by using the p (<0.05) value and Tukey’s HSD bar in the figures. The error bars and letters to show significance were purposely removed as the line graphs got clumsier and were difficult to distinguish.
6. In Fig. 1 the legends LMA, SMA, MIC and MIN have now been clearly explained in figure caption. The four different aggregate classes have been abbreviated as LMA, SMA, MIC and MIN which have been updated as “Large macro aggregates, small macroaggregates, microaggregates and silt+clay”.