Agrochemicals and Shade Complexity Affect Soil Quality in Coffee Home Gardens
, K. A. I. Nekaris 1,*, Andrew Rendell 2, Budiadi Budiadi 3, Muhammad Ali Imron 3 and Marco Campera 2
Round 1
Reviewer 1 Report
- A brief summary
The subject of this manuscript is very interesting and provides a valuable contribution to the sustainable production of coffee in home gardens and the importance of high shade complexity in these systems. The study also highlights the significance of organic fertilization practices in increasing soil quality.
- General concept comments
The authors should specify what the organic practices and particularly the organic fertilizers used by farmers in the study. Are farms categorized as “organic” using commercially available organic fertilizers, locally sourced manures or do they make their own compost from coffee production crop residues or coffee production waste? The authors mention that waste from coffee processing can help increase pH and the presence of Mg and K. Are any of the farmers interviewed use this practice? Also, the average length of using organic practices should be indicated.
It would be helpful to analyze the interaction of agrochemical use with shade complexity. Do farmers with Higher shade complexity use predominantly organic inputs, while Sun farmers use predominantly agrochemical inputs? Could the interaction of agrochemical use with shade complexity better explain some of the observed variation in values in the study?
- Specific comments
Line 24: The authors say in the abstract that they advocate for the use of “high-quality organic fertilizers”, but they don’t discuss what they define as “high-quality” organic fertilizers anywhere in the manuscript.
Line 24: The authors state that “organic gardens had less important nutrients than gardens using agrochemicals”. Do they mean that they had less of the important nutrients or nutrients of a lesser importance? This needs to be rephrased to make it clear.
Line 109: The authors point to a previous publication for info on the types of agrochemicals used but given that this information is important for this study, they should be included here too. It is particularly important to indicate the types of organic fertilizers used.
Line 128:. The authors mention that available phosphorus was determined in their soil analysis, but they don’t show any data on phosphorus levels in the various farms in their study
Line 185: The authors analyzed the effect of Shade complexity on C:N ratio of soil samples in Figure 4, but they didn’t show any data on the effect of organic fertilizers on C:N ratio. As organic fertilizers contain organic matter, they can also be contributing to the changes in soi C:N ratios.
Line 217: The authors state that “Whilst pH was generally lower in farms that had lower shade complexity, low pH was also observed in medium and high shade complexity farms”. Which are the “medium shade complexity” farms? In the Materials & Methods only three shade complexity farms are defined: High shade complexity, Low shade complexity & Sun. There should be standard terminology of shade complexity farms to avoid confusion.
Line 218: The authors state that “high shade complexity farms showing the largest amount of variation”. From Figure 3 it appears that Sun farms show the largest amount of variation. Could the observed variation in soil pH values in Sun farms be attributed to wider variation in fertilizer types used (organic and chemical) compared to High shade complexity farms who might use more organic fertilizers?
Line 249: The authors again use different terminology for shade complexity (…farms with high, medium and low shade complexity). There should be standard terminology of shade complexity farms throughout the manuscript to avoid confusion.
Line 265: The authors mention that “soil samples were collected the same year as organic farming practices were implemented’”. Does this apply to all farms categorized as “organic”? Were these farms using agrochemicals the previous year? If so, they should make this clear in the Material & Methods section.
Author Response
Reviewer 1
A brief summary
The subject of this manuscript is very interesting and provides a valuable contribution to the sustainable production of coffee in home gardens and the importance of high shade complexity in these systems. The study also highlights the significance of organic fertilization practices in increasing soil quality.
General concept comments
The authors should specify what the organic practices and particularly the organic fertilizers used by farmers in the study. Are farms categorized as “organic” using commercially available organic fertilizers, locally sourced manures or do they make their own compost from coffee production crop residues or coffee production waste? The authors mention that waste from coffee processing can help increase pH and the presence of Mg and K. Are any of the farmers interviewed use this practice? Also, the average length of using organic practices should be indicated.
- We appreciate the intention of the reviewer to add greater clarification to our use of the term “organic” within the context of our study site. We have taken this on board and have implemented this into our paper, as explained in the following comments.
It would be helpful to analyze the interaction of agrochemical use with shade complexity. Do farmers with Higher shade complexity use predominantly organic inputs, while Sun farmers use predominantly agrochemical inputs? Could the interaction of agrochemical use with shade complexity better explain some of the observed variation in values in the study?
- The reviewer is right, we have now tested whether there was an association between shade complexity and agrochemical use but found none. We cannot add an interaction effect term in the model as that would reduce the degrees of freedom, and we have a relatively small sample size. Also, some groups are underrepresented (<5 samples) so not enough to get a variance.
Specific comments
Line 24: The authors say in the abstract that they advocate for the use of “high-quality organic fertilizers”, but they don’t discuss what they define as “high-quality” organic fertilizers anywhere in the manuscript.
- We appreciate the reviewer’s comment as we did not clearly define “high-quality organic fertilizers”, Instead, we have moved this to the discussion in order to shorten the abstract and to ensure we have correctly defined what “high-quality organic fertilizers” we will be promoting (see line 327).
Line 24: The authors state that “organic gardens had less important nutrients than gardens using agrochemicals”. Do they mean that they had less of the important nutrients or nutrients of a lesser importance? This needs to be rephrased to make it clear.
- This sentence has since been removed.
Line 109: The authors point to a previous publication for info on the types of agrochemicals used but given that this information is important for this study, they should be included here too. It is particularly important to indicate the types of organic fertilizers used.
- In the line the reviewer is referring to, we are only establishing whether agrochemicals were used, and not what agrochemicals were used. However, we appreciate that we need to include what agrochemicals farmers within our study area use, and these have now been added to the introduction as context for the study (see line 110).
Line 128:. The authors mention that available phosphorus was determined in their soil analysis, but they don’t show any data on phosphorus levels in the various farms in their study
- We thank the reviewer for noticing this as this was a mistake on our part and has now been removed.
Line 185: The authors analyzed the effect of Shade complexity on C:N ratio of soil samples in Figure 4, but they didn’t show any data on the effect of organic fertilizers on C:N ratio. As organic fertilizers contain organic matter, they can also be contributing to the changes in soi C:N ratios.
- We appreciate that organic fertilizers will have been having an effect on C:N ratio; however, this finding was not significant, as shown in Table 1, therefore we did not make a figure detailing the results.
Line 217: The authors state that “Whilst pH was generally lower in farms that had lower shade complexity, low pH was also observed in medium and high shade complexity farms”. Which are the “medium shade complexity” farms? In the Materials & Methods only three shade complexity farms are defined: High shade complexity, Low shade complexity & Sun. There should be standard terminology of shade complexity farms to avoid confusion.
- We thank the reviewer for this comment as this was a mistake on our part. “Medium” has now been changed to “low” (see line 220).
Line 218: The authors state that “high shade complexity farms showing the largest amount of variation”. From Figure 3 it appears that Sun farms show the largest amount of variation. Could the observed variation in soil pH values in Sun farms be attributed to wider variation in fertilizer types used (organic and chemical) compared to High shade complexity farms who might use more organic fertilizers?
- First of all, we appreciate the reviewer’s comment that it was in fact sun farms that had the most observed variation. We agree with the reviewer’s interpretation of the variation observed in sun farms and have added this to the end of the paragraph (see line 232).
Line 249: The authors again use different terminology for shade complexity (…farms with high, medium and low shade complexity). There should be standard terminology of shade complexity farms throughout the manuscript to avoid confusion.
- We thank the reviewer for their comment as this was, again, a mistake on our part. “Medium” has now been changed to “low”, and “low” has now been changed to “sun”.
Line 265: The authors mention that “soil samples were collected the same year as organic farming practices were implemented’”. Does this apply to all farms categorized as “organic”? Were these farms using agrochemicals the previous year? If so, they should make this clear in the Material & Methods section.
- We appreciate this comment from the reviewer as this is valuable context for the study. Therefore, we have added that organic practices were present prior to the implementation of natural pest control and rabbit manure in 2019 (see line 275).
We would like to thank the reviewer for their detailed comments and appreciate the valuable contributions they have made to our paper.
Reviewer 2 Report
The subject of the manuscript is suitable to the Journal. The paper adds new and original values to the science.
The keywords correspond well to the scope of the research.
I think the paper needs some corrections. You should add some information and references to the paper because:
1) the Abstract is too long,
2) the research hypotheses have not been clearly formulated,
3) add information about analytical quality control,
4) add units to Y axis in Figures 1 and 5,
5) add references to all analytical and statistical methods to Materials and Methods section,
6) rewrite Conclusions and Abstracts,
7) why you not used typical statistical calculations for experimental research?,
8) add results of statistical analysis to Table 1, e.g. standard deviation,
9) why other macronutrients were not analyzed?
10) standardize References section,
11) paper needs some editorial corrections (see: Instructions for Authors).
Conclusions are poorly written. Conclusions should only concern the results obtained in your research and their importance in science (or agricultural production). Part of the text from Conclusions should be moved to the Discussion section.
You must check your paper very exactly, correct all other mistakes, add the necessary information and standardize References section of paper.
Author Response
Reviewer 2
The subject of the manuscript is suitable to the Journal. The paper adds new and original values to the science.
The keywords correspond well to the scope of the research.
I think the paper needs some corrections. You should add some information and references to the paper because:
- the Abstract is too long,
- We appreciate the reviewer’s comment and in trying to make the abstract more concise, we have reduced it by 20 words.
2) the research hypotheses have not been clearly formulated,
- We have reviewed our research hypotheses and agree that one of our hypotheses regarding the toxicity of soils was missing, and this has now been added (see line 96). We now believe that our hypotheses have been clearly formulated.
3) add information about analytical quality control,
- As specified, the analysis was performed by an accredited lab that is using standard methods and performs quality control. We have now added more information.
4) add units to Y axis in Figures 1 and 5,
- These have now been added.
5) add references to all analytical and statistical methods to Materials and Methods section,
- We believe that we have now added all the references.
6) rewrite Conclusions and Abstracts,
- We have edited the Conclusion and Abstract.
7) why you not used typical statistical calculations for experimental research?
- We are not sure we understand this comment as we believe that Generalised Linear Models are standard methods of data analysis. The use of more basic tests such as t-tests is not advised in our case because we have more than two groups and most of the variables are not normally distributed.
8) add results of statistical analysis to Table 1, e.g. standard deviation,
- We have now added the standard error to Table 1.
9) why other macronutrients were not analyzed?
- We selected the macronutrients we believed to be important for coffee growth and soil quality, and those that were most likely to be influenced by agrochemical use/shade complexity.
10) standardize References section,
- We have removed the DOI of one cited articles as this was not in line with the rest of the reference list, but we kept the doi for another as it is not published in a volume yet.
11) paper needs some editorial corrections (see: Instructions for Authors).
- We are not sure about this comment, which editorial corrections are needed?
Conclusions are poorly written. Conclusions should only concern the results obtained in your research and their importance in science (or agricultural production). Part of the text from Conclusions should be moved to the Discussion section.
- We agree with the reviewer that the authors missed the scope of the conclusions and, as suggested by the reviewer, we have moved part of the conclusions to the discussion (see line 272) and have elaborated on our results at the start of the conclusions section (see line 288).
You must check your paper very exactly, correct all other mistakes, add the necessary information and standardize References section of paper.
- We would like to thank the reviewer for their detailed comments and appreciate the valuable contributions they have made to our paper.
Reviewer 3 Report
The manuscript contains quite interesting research results. Requires minor adjustments.
Comments:
Citation: Lastname, F.; Lastname, F.; Lastname, F. Title. ?
Line 30, correct soil organic carbon
Line 104, correct 30 cm
Line 127, correct soil organic carbon (SOC)
Line 144, please provide full details of the manufacturer of the statistical software
Table 1, correct pH (H2O)
5. Conclusions are too long.
References, please remove the oldest publications, before 2010 (1, 2, 15, 18, 21, 29, 35, 37, 44, 47, 50).
Author Response
Reviewer 3
The manuscript contains quite interesting research results. Requires minor adjustments.
Comments:
Citation: Lastname, F.; Lastname, F.; Lastname, F. Title. ?
- This will be filled by the editorial office after acceptance.
Line 30, correct soil organic carbon
- We appreciate the reviewers comment as without the addition of “soil”, this key word could be interpreted differently.
Line 104, correct 30 cm
- This has been corrected.
Line 127, correct soil organic carbon (SOC)
- Although we appreciate the reviewer’s intention to clarify what carbon we are referring to, as this is in the soil sample analysis section, we are referencing it the way we received the results, i.e., carbon (C).
Line 144, please provide full details of the manufacturer of the statistical software
- Citation has been added.
Table 1, correct pH (H2O)
- This has been corrected.
- Conclusions are too long.
- We appreciate this comment and the conclusion section has now been reduced by around a third.
References, please remove the oldest publications, before 2010 (1, 2, 15, 18, 21, 29, 35, 37, 44, 47, 50).
- We would like to keep them as they provide an invaluable contribution to our paper. We believe that it is a standard procedure to cite papers from early 2000s. We do not think that we have old references.
We would like to thank the reviewer for their detailed comments and appreciate the valuable contributions they have made to our paper.
Reviewer 4 Report
The paper presents a comparative study of soil quality for coffee plantations in Indonesia. The information presented has utility for coffee, and other tree crops such as cocoa.
The writing is fine. I could quibble and suggest that the use of the pronoun "We" should be reduced.
It would be useful to add a comment about the "agrochemicals" that were used by the farms. The chemical use reduces soil pH, and the lower pH increases the solubility of metals. Urea has a high pH; DKP has a pH nearer 8. Potash (KCl) makes the soil more saline - and that could be link to the lower pH. It would be useful if a note could be added about the types of chemicals used.
Also - the analysis of soil pH by chemical use, and the impact of shade trees are not linked. Are the chemical users/organic users evenly distributed across the shade farms? Is it possible to see if these two populations are linked - or at least to mention that it was investigated, but that nothing could be found.
Otherwise - the paper is ready for publication.
Author Response
Reviewer 4
The paper presents a comparative study of soil quality for coffee plantations in Indonesia. The information presented has utility for coffee, and other tree crops such as cocoa.
The writing is fine. I could quibble and suggest that the use of the pronoun "We" should be reduced.
- We use the active voice as this is suggested by most journals.
It would be useful to add a comment about the "agrochemicals" that were used by the farms. The chemical use reduces soil pH, and the lower pH increases the solubility of metals. Urea has a high pH; DKP has a pH nearer 8. Potash (KCl) makes the soil more saline - and that could be link to the lower pH. It would be useful if a note could be added about the types of chemicals used.
- We appreciate the reviewer’s comment in relation to adding information about the specific agrochemicals used in the study area, and this has now been added (see line 110).
Also - the analysis of soil pH by chemical use, and the impact of shade trees are not linked. Are the chemical users/organic users evenly distributed across the shade farms? Is it possible to see if these two populations are linked - or at least to mention that it was investigated, but that nothing could be found.
- We appreciate the reviewer’s perspective regarding the link between agrochemicals and shade farms. Although there is a relationship between shade farms and organic practices, this is not evenly distributed throughout the study area, and sun farms use a range of agrochemicals and organic alternatives. We agree that this is a useful note to add and the this has been added to the methods (see line 123).
Otherwise - the paper is ready for publication.
- We would like to thank the reviewer for their detailed comments and appreciate the valuable contributions they have made to our paper.
Round 2
Reviewer 2 Report
The authors addressed most reviewer comments or gave the explanations. All sections are rather good.
The manuscript entitled “Agrochemicals and shade complexity affect soil quality in coffee home gardens” can be accepted for publishing in Earth.
