the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
18 Jan 2021
18 Jan 2021
Estimation of soil properties with mid-infrared soil spectroscopy across yam production landscapes in West Africa
- 1Group of Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zurich, 8092 Zürich, Switzerland
- 2Department of Agronomy and Medicinal Plant Resources, Gyeongnam National University of Science and Technology, Jinju, Republic of Korea
- 3Group of Plant Nutrition, Institute of Agricultural Sciences, ETH Zurich, 8315 Lindau, Switzerland
- 4World Agroforestry Centre (ICRAF), Côte d’Ivoire Country Programme, BP 2823 Abidjan, Ivory Coast
- 5Centre Suisse de Recherches Scientifiques en Côte d’ivoire, 01 BP 1303 Abidjan, Ivory Coast
- 6Département d’Agrophysiologie des Plantes, Université Peleforo Gon Coulibaly, BP 1328 Korhogo, Ivory Coast
- 7Institut de l’Environnement et Recherches Agricoles, 01 BP 476 Ouagadougou, Burkina Faso
- 8Land Health Decisions, World Agroforestry Centre (ICRAF), Nairobi, Kenya
- 1Group of Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zurich, 8092 Zürich, Switzerland
- 2Department of Agronomy and Medicinal Plant Resources, Gyeongnam National University of Science and Technology, Jinju, Republic of Korea
- 3Group of Plant Nutrition, Institute of Agricultural Sciences, ETH Zurich, 8315 Lindau, Switzerland
- 4World Agroforestry Centre (ICRAF), Côte d’Ivoire Country Programme, BP 2823 Abidjan, Ivory Coast
- 5Centre Suisse de Recherches Scientifiques en Côte d’ivoire, 01 BP 1303 Abidjan, Ivory Coast
- 6Département d’Agrophysiologie des Plantes, Université Peleforo Gon Coulibaly, BP 1328 Korhogo, Ivory Coast
- 7Institut de l’Environnement et Recherches Agricoles, 01 BP 476 Ouagadougou, Burkina Faso
- 8Land Health Decisions, World Agroforestry Centre (ICRAF), Nairobi, Kenya
Abstract. Low soil fertility is challenging the sustainable production of staple crops in the yam belt of West Africa. Quantitative soil measures are needed to assess soil fertility decline and to improve crop fertilization management in the region. We developed and tested a mid-infrared (mid-IR) soil spectral library to enable timely and cost-efficient assessments of soil properties. Our collection included 80 soil samples from four landscapes (10 km × 10 km) and 20 fields/landscape across a gradient from humid forest to savanna, and 14 additional samples from one landscape that had been sampled within the Land Health Degradation Framework. We derived partial least square regression models to estimate soil properties with spectra.The models produced accurate cross-validated estimates of total carbon, total nitrogen, total sulfur, total iron, total aluminum, total potassium, total calcium, exchangeable calcium, effective cation exchange capacity, diethylenetriaminepentaacetic acid (DTPA) extractable iron and clay content (R2 > 0.75). The estimates of total zinc, pH, exchangeable magnesium, bioavailable copper and manganese were less predictable (R2 > 0.50). Our results confirm that mid-IR spectroscopy is a reliable and quick method assess the regional-scale variation in most soil properties, especially the ones closely associated with soil organic matter. Although the relatively small mid-IR library shows satisfactory performance, we expect that frequent but small model updates will be needed to adapt the library to the variation of soil quality attributes within individual fields in the regions and their temporal fluctuations.
Philipp Baumann et al.
Status: final response (author comments only)
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AC1: 'Comment on soil-2020-100', Philipp Baumann, 20 Jan 2021
This preprint should not contain chemical reference data and model outputs of plant-available Phosphorus (P) derived with the anion exchange resin method (resin extractable P), but the current upload of the manuscript was produced from a previous PDF file that accidentally still contained these data. The reason is that further sampling events and resin P analyses conducted in one of the project regions indicated that more resin membranes were necessary to correctly represent values for soils with rather high extractability of P. There is no modification of the upload possible at the current stage of review since the manuscript has already been posted for interactive discussion. As a precautionary measure, we will hence upload the updated version of the manuscript following the first round of review, which will be without these results and the discussion around it. We apologize for the inconvenience and are looking forward to the feedback of the reviewers and the community.
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EC1: 'Comment on soil-2020-100', Stefan Hauser, 18 Apr 2021
The manuscript tackles an important issue: yam production is marred by declining yields and a lack of positive fertilizer responses, the absence of current fertilizer recommendations and generally old and traditional cropping systems and technologies.
The title somehow promises to be yam specific, yet the manuscript does not really produce data or results that would be specific to any crop. Although this is not a short fall, I would recommend that the authors reflect upon the need to have yam as a target crop – sure the samples were taken in yam fields and this could be taken as a reason, yet not a strong one.
The set of chemical variables (elements) measured is rather wide and gives the impression it was done because it was possible. The manuscript does not give any indication of how important these elements are for yam growth and yield, except for N and K in a by-sentence. Although the focus of the manuscript is clearly on the IR predictions and models, the manuscript would gain quality if nutrient requirements of yam and the problems of yam plant nutrition were considered to a larger extend.
I would appreciate it if the authors added a short section on which of the accurately predictable chemical or physical properties and elements would be of importance to monitor soil quality for yam. In addition a critical assessment of the differences between total element and available element data – which one matters more?
To talk about West Africa (Senegal to Cameroon – all yam producing countries) after sampling in two countries is as well somewhat far-fetched. The authors may consider a change in the title.
The manuscript has several highlighted text portions the comments in detail on these portions are either in the note boxes or below.
Page 2 line 20: population growth does not cause soil degradation it is the increased land use frequency and intensity that causes soil degradation.
Combine with previous sentence to create a correct statement.
Page 2 line 25 – A particularly strong positive …..
Page 2 line 31: into the physical, chemical and biological major components
Page 2 line 36: not only mineral fertilizer but as well the soils’ inherent fertility or nutrient status. Additional factors are the tillage regime, the planting date, staking, and stake height see: Enesi, O.R., Hauser, S., Lopez-Montez, A., Osunobi, O. (2018) Yam Tuber and Maize Grain Yield Response to Cropping System Intensification in South-West Nigeria. Archives of Agronomy and Soil Science, 64:7, 953-966.
Page 2 line 48 is it really the case that the IR approaches complement the wet chemistry or is it more that the IR approach requires the wet chemistry to make sense of the spectra?
Page 2 line 52 is it only often that IR spectroscopy needs wet chemistry references or is it more that currently they are the essential part of interpreting the spectra?
Page 4 line 89 YAMSYS in full please
Page 16 line 273 I would challenge the importance of SOC to store water – it is mainly the soil texture that determines water holding capacity, whereby SOC may play a positive role in aggregation and thus improve water holding capacity yet it is not primarily the “body” holding water. Please rephrase or remove the water
Page 16 line 275 – land use pressure is a bad term what we look at is a higher land use frequency and shorter fallow – please rephrase accordingly.
Page 16 line 276 – the sentence is too long and combines too many factors. It is correct that fallow and slash and burn go together, with the burning at least partially destroying the C input to the soil – please phrase to show the consequences of the cropping system in brief – monitoring the soil quality is a different aspect and would need being discussed in connection with the farm households ability to engage with such activities.
Page 16 line 278 – this sounds like closing the yield gap is a process that simply runs parallel to improving soil quality, however it would be the consequence and not something that happens automatically. Please break down the long sentence and separate cause and effect here. It would be of particular importance to clearly single out the monitoring of soil properties from activities improving soil properties – make sure it is clear that there are tools to improve soil quality and tools to monitor soil quality.
Page 16 line 281 - Proposed sentence: To give a specific example, yam requires relatively large quantities of N and K (e.g., O’Sullivan, 2010); on light-textured soils yam can attain high tuber yields but at a high risk of losing large proportions of applied N and K, to the environment (e.g., Diby et al., 2011).
To be considered here is that if a large portion of N and K are lost yields are unlikely to be high.
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RC1: 'Comment on soil-2020-100', Anonymous Referee #1, 20 Apr 2021
The manuscript evaluated the potential of mid-infrared (MIR) soil spectroscopy in estimating a comprehensive list of soil properties in West Africa. The cross-validation of partial least square regression (PLSR) indicated that 11 soil properties can be accurately estimated (R2>0.75) while the predictions of other soil properties were less accurate. The manuscript is overall well written with solid methodology (in terms of model parameter optimization and validation strategy). However, the manuscript does not provide new insights to the community as MIR has been studied a lot in soil spectral prediction across scales and the PLSR model is a commonly used linear model. I suggest the authors redefine the objectives of this study in order to highlight the knowledge gap that this manuscript deals with. In addition, I would like to see more discussions about the pros and cons among lab MIR, lab vis-NIR, and in-situ spectroscopy as I am quite sure that the measurement of MIR mentioned in this study is still time-consuming (preparation of fine ground potassium bromide powder). Please find my detailed suggestions below.
Line 67: The map of soil sampling sites is missing. This is a really helpful message to readers.
Lines 116-118: I have a big question here that is it really necessary to predict total elements by MIR spectra as you used the reference measurements from energy dispersive X-ray fluorescence spectrometry (ED-XRF) which does not require much more cost or time than MIR spectroscopy. So why not directly use the measurements from ED-XRF which have better quality?
Line 144: 128 measurements? I am confused here as there are only 94 milled soil samples.
Line 153: I recommend adding the use of a non-linear model (e.g., Cubist, Random Forest) to better demonstrate the predictive ability of MIR.
Line 172: The definition of Sy is missing in equation 2.
Lines 174-155: Until the end of this manuscript, I did not see any results relevant to the uncertainty analysis mentioned here.
Lines 206: As shown in Figure 1, a large difference in soil properties were observed from four regions. Maybe it would be an interesting part to discuss whether the model build from three regions can be applicable to the remaining region.
Line 297: Please check a highly relevant paper (see below) which indicated a good model performance of MIR spectral models to a list of soil properties at a national scale. In addition, Rossel should be corrected as Viscarra Rossel. Please also check the relevant typos (e.g., line 299).
Sanderman, J., Savage, K., & Dangal, S. R. (2020). Midâinfrared spectroscopy for prediction of soil health indicators in the United States. Soil Science Society of America Journal, 84(1), 251-261.
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RC2: 'Comment on soil-2020-100', Stefan Hauser, 23 Apr 2021
Comments on manuscript soil-2020-100
The manuscript tackles an important issue: yam production is marred by declining yields and a lack of positive fertilizer responses, the absence of current fertilizer recommendations and generally old and traditional cropping systems and technologies.
The title somehow promises to be yam specific, yet the manuscript does not really produce data or results that would be specific to any crop. Although this is not a short fall, I would recommend that the authors reflect upon the need to have yam as a target crop – sure the samples were taken in yam fields and this could be taken as a reason, yet not a strong one.
The set of chemical variables (elements) measured is rather wide and gives the impression it was done because it was possible. The manuscript does not give any indication of how important these elements are for yam growth and yield, except for N and K in a by-sentence. Although the focus of the manuscript is clearly on the IR predictions and models, the manuscript would gain quality if nutrient requirements of yam and the problems of yam plant nutrition were considered to a larger extend.
I would appreciate it if the authors added a short section on which of the accurately predictable chemical or physical properties and elements would be of importance to monitor soil quality for yam. In addition a critical assessment of the differences between total element and available element data – which one matters more?
To talk about West Africa (Senegal to Cameroon – all yam producing countries) after sampling in two countries is as well somewhat far-fetched. The authors may consider a change in the title.
The manuscript has several highlighted text portions the comments in detail on these portions are either in the note boxes or below.
Page 2 line 20: population growth does not cause soil degradation it is the increased land use frequency and intensity that causes soil degradation.
Combine with previous sentence to create a correct statement.
Page 2 line 25 – A particularly strong positive …..
Page 2 line 31: into the physical, chemical and biological major components
Page 2 line 36: not only mineral fertilizer but as well the soils’ inherent fertility or nutrient status. Additional factors are the tillage regime, the planting date, staking, and stake height see: Enesi, O.R., Hauser, S., Lopez-Montez, A., Osunobi, O. (2018) Yam Tuber and Maize Grain Yield Response to Cropping System Intensification in South-West Nigeria. Archives of Agronomy and Soil Science, 64:7, 953-966.
Page 2 line 48 is it really the case that the IR approaches complement the wet chemistry or is it more that the IR approach requires the wet chemistry to make sense of the spectra?
Page 2 line 52 is it only often that IR spectroscopy needs wet chemistry references or is it more that currently they are the essential part of interpreting the spectra?
Page 4 line 89 YAMSYS in full please
Page 16 line 273 I would challenge the importance of SOC to store water – it is mainly the soil texture that determines water holding capacity, whereby SOC may play a positive role in aggregation and thus improve water holding capacity yet it is not primarily the “body” holding water. Please rephrase or remove the water
Page 16 line 275 – land use pressure is a bad term what we look at is a higher land use frequency and shorter fallow – please rephrase accordingly.
Page 16 line 276 – the sentence is too long and combines too many factors. It is correct that fallow and slash and burn go together, with the burning at least partially destroying the C input to the soil – please phrase to show the consequences of the cropping system in brief – monitoring the soil quality is a different aspect and would need being discussed in connection with the farm households ability to engage with such activities.
Page 16 line 278 – this sounds like closing the yield gap is a process that simply runs parallel to improving soil quality, however it would be the consequence and not something that happens automatically. Please break down the long sentence and separate cause and effect here. It would be of particular importance to clearly single out the monitoring of soil properties from activities improving soil properties – make sure it is clear that there are tools to improve soil quality and tools to monitor soil quality.
Page 16 line 281 - Proposed sentence: To give a specific example, yam requires relatively large quantities of N and K (e.g., O’Sullivan, 2010); on light-textured soils yam can attain high tuber yields but at a high risk of losing large proportions of applied N and K, to the environment (e.g., Diby et al., 2011).
To be considered here is that if a large portion of N and K are lost yields are unlikely to be high
Philipp Baumann et al.
Data sets
philipp-baumann/yamsys-soilspec-publication: Pre-release of spectral models for the publication of the soil spectral library of the West African yam belt (Version v0.1.0-beta). Zenodo Philipp Baumann https://doi.org/10.5281/zenodo.1174869
Model code and software
philipp-baumann/simplerspec: Beta release simplerspec 0.1.0 for zenodo (Version v0.1.0-beta). Zenodo Philipp Baumann https://doi.org/10.5281/zenodo.3303637
Philipp Baumann et al.
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